1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/29680fa5c35e/ changeset: 29680fa5c35e user: jgoecks date: 2012-08-07 15:40:51 summary: Use mako template in tool help so that dynamic image paths can be used. Fixes #141 affected #: 58 files diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -8,6 +8,7 @@ import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback import simplejson import binascii +from mako.template import Template from UserDict import DictMixin from galaxy.util.odict import odict from galaxy.util.bunch import Bunch @@ -1068,7 +1069,8 @@ break def parse_help( self, root ): """ - Parse the help text for the tool. Formatted in reStructuredText. + Parse the help text for the tool. Formatted in reStructuredText, but + stored as Mako to allow for dynamic image paths. This implementation supports multiple pages. """ # TODO: Allow raw HTML or an external link. @@ -1080,7 +1082,7 @@ help_pages = self.help.findall( "page" ) help_header = self.help.text try: - self.help = util.rst_to_html(self.help.text) + self.help = Template( util.rst_to_html(self.help.text) ) except: log.exception( "error in help for tool %s" % self.name ) # Multiple help page case @@ -1090,7 +1092,7 @@ help_footer = help_footer + help_page.tail # Each page has to rendered all-together because of backreferences allowed by rst try: - self.help_by_page = [ util.rst_to_html( help_header + x + help_footer ) + self.help_by_page = [ Template( util.rst_to_html( help_header + x + help_footer ) ) for x in self.help_by_page ] except: log.exception( "error in multi-page help for tool %s" % self.name ) diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -332,6 +332,9 @@ else: tool_help = tool.help + # Help is Mako template, so render using current static path. + tool_help = tool_help.render( static_path=h.url_for( '/static' ) ) + # Convert to unicode to display non-ascii characters. if type( tool_help ) is not unicode: tool_help = unicode( tool_help, 'utf-8') diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/discreteWavelet/execute_dwt_IvC_all.xml --- a/tools/discreteWavelet/execute_dwt_IvC_all.xml +++ b/tools/discreteWavelet/execute_dwt_IvC_all.xml @@ -101,11 +101,11 @@ The second output file: -.. image:: ./static/operation_icons/dwt_IvC_1.png -.. image:: ./static/operation_icons/dwt_IvC_2.png -.. image:: ./static/operation_icons/dwt_IvC_3.png -.. image:: ./static/operation_icons/dwt_IvC_4.png -.. image:: ./static/operation_icons/dwt_IvC_5.png +.. image:: ${static_path}/operation_icons/dwt_IvC_1.png +.. image:: ${static_path}/operation_icons/dwt_IvC_2.png +.. image:: ${static_path}/operation_icons/dwt_IvC_3.png +.. image:: ${static_path}/operation_icons/dwt_IvC_4.png +.. image:: ${static_path}/operation_icons/dwt_IvC_5.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/discreteWavelet/execute_dwt_cor_aVa_perClass.xml --- a/tools/discreteWavelet/execute_dwt_cor_aVa_perClass.xml +++ b/tools/discreteWavelet/execute_dwt_cor_aVa_perClass.xml @@ -101,11 +101,11 @@ The second output file: -.. image:: ./static/operation_icons/dwt_cor_aVa_1.png -.. image:: ./static/operation_icons/dwt_cor_aVa_2.png -.. image:: ./static/operation_icons/dwt_cor_aVa_3.png -.. image:: ./static/operation_icons/dwt_cor_aVa_4.png -.. image:: ./static/operation_icons/dwt_cor_aVa_5.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_1.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_2.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_3.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_4.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_5.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/discreteWavelet/execute_dwt_cor_aVb_all.xml --- a/tools/discreteWavelet/execute_dwt_cor_aVb_all.xml +++ b/tools/discreteWavelet/execute_dwt_cor_aVb_all.xml @@ -106,16 +106,16 @@ The second output file: -.. image:: ./static/operation_icons/dwt_cor_aVb_all_1.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_2.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_3.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_4.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_5.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_6.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_7.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_8.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_9.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_10.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_1.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_2.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_3.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_4.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_5.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_6.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_7.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_8.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_9.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_10.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/discreteWavelet/execute_dwt_var_perClass.xml --- a/tools/discreteWavelet/execute_dwt_var_perClass.xml +++ b/tools/discreteWavelet/execute_dwt_var_perClass.xml @@ -98,7 +98,7 @@ The third output file: -.. image:: ./static/operation_icons/dwt_var_perClass.png +.. image:: ${static_path}/operation_icons/dwt_var_perClass.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/evolution/add_scores.xml --- a/tools/evolution/add_scores.xml +++ b/tools/evolution/add_scores.xml @@ -43,8 +43,8 @@ The input can be any interval_ format dataset. The output is also in interval format. (`Dataset missing?`_) -.. _interval: ./static/formatHelp.html#interval -.. _Dataset missing?: ./static/formatHelp.html +.. _interval: ${static_path}/formatHelp.html#interval +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/evolution/codingSnps.xml --- a/tools/evolution/codingSnps.xml +++ b/tools/evolution/codingSnps.xml @@ -94,9 +94,9 @@ The gene dataset is in BED_ format with 12 columns. The output dataset is also interval. (`Dataset missing?`_) -.. _interval: ./static/formatHelp.html#interval -.. _BED: ./static/formatHelp.html#bed -.. _Dataset missing?: ./static/formatHelp.html +.. _interval: ${static_path}/formatHelp.html#interval +.. _BED: ${static_path}/formatHelp.html#bed +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/fastx_toolkit/fasta_clipping_histogram.xml --- a/tools/fastx_toolkit/fasta_clipping_histogram.xml +++ b/tools/fastx_toolkit/fasta_clipping_histogram.xml @@ -1,6 +1,6 @@ <tool id="cshl_fasta_clipping_histogram" name="Length Distribution"><description>chart</description> - <requirements><requirement type="package">fastx_toolkit</requirement></requirements> + <requirements><requirement type="package">fastx_toolkit</requirement></requirements><command>fasta_clipping_histogram.pl $input $outfile</command><inputs> @@ -25,13 +25,13 @@ In the following library, most sequences are 24-mers to 27-mers. This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place). -.. image:: ./static/fastx_icons/fasta_clipping_histogram_1.png +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_1.png In the following library, most sequences are 19,22 or 23-mers. This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place). -.. image:: ./static/fastx_icons/fasta_clipping_histogram_2.png +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_2.png ----- @@ -81,7 +81,7 @@ Each sequence is counts as one, to produce the following chart: -.. image:: ./static/fastx_icons/fasta_clipping_histogram_3.png +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_3.png Example 2 - The following FASTA file have multiplicity counts:: @@ -95,7 +95,7 @@ The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart: -.. image:: ./static/fastx_icons/fasta_clipping_histogram_4.png +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_4.png Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts. diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/fastx_toolkit/fastq_quality_boxplot.xml --- a/tools/fastx_toolkit/fastq_quality_boxplot.xml +++ b/tools/fastx_toolkit/fastq_quality_boxplot.xml @@ -32,16 +32,16 @@ An excellent quality library (median quality is 40 for almost all 36 cycles): -.. image:: ./static/fastx_icons/fastq_quality_boxplot_1.png +.. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_1.png A relatively good quality library (median quality degrades towards later cycles): -.. image:: ./static/fastx_icons/fastq_quality_boxplot_2.png +.. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_2.png A low quality library (median drops quickly): -.. image:: ./static/fastx_icons/fastq_quality_boxplot_3.png +.. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_3.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/fastx_toolkit/fastx_barcode_splitter.xml --- a/tools/fastx_toolkit/fastx_barcode_splitter.xml +++ b/tools/fastx_toolkit/fastx_barcode_splitter.xml @@ -1,6 +1,6 @@ <tool id="cshl_fastx_barcode_splitter" name="Barcode Splitter"><description></description> - <requirements><requirement type="package">fastx_toolkit</requirement></requirements> + <requirements><requirement type="package">fastx_toolkit</requirement></requirements><command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output </command><inputs> @@ -62,7 +62,7 @@ **Output Example** -.. image:: ./static/fastx_icons/barcode_splitter_output_example.png +.. image:: ${static_path}/fastx_icons/barcode_splitter_output_example.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/fastx_toolkit/fastx_clipper.xml --- a/tools/fastx_toolkit/fastx_clipper.xml +++ b/tools/fastx_toolkit/fastx_clipper.xml @@ -1,6 +1,6 @@ <tool id="cshl_fastx_clipper" name="Clip" version="1.0.1" ><description>adapter sequences</description> - <requirements><requirement type="package">fastx_toolkit</requirement></requirements> + <requirements><requirement type="package">fastx_toolkit</requirement></requirements><command> zcat -f $input | fastx_clipper -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS #if $input.ext == "fastqsanger": @@ -82,7 +82,7 @@ **Clipping Illustration:** -.. image:: ./static/fastx_icons/fastx_clipper_illustration.png +.. image:: ${static_path}/fastx_icons/fastx_clipper_illustration.png @@ -93,7 +93,7 @@ **Clipping Example:** -.. image:: ./static/fastx_icons/fastx_clipper_example.png +.. image:: ${static_path}/fastx_icons/fastx_clipper_example.png diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/fastx_toolkit/fastx_nucleotides_distribution.xml --- a/tools/fastx_toolkit/fastx_nucleotides_distribution.xml +++ b/tools/fastx_toolkit/fastx_nucleotides_distribution.xml @@ -1,6 +1,6 @@ <tool id="cshl_fastx_nucleotides_distribution" name="Draw nucleotides distribution chart"><description></description> - <requirements><requirement type="package">fastx_toolkit</requirement></requirements> + <requirements><requirement type="package">fastx_toolkit</requirement></requirements><command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command><inputs> @@ -26,19 +26,19 @@ The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT** -.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_1.png +.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_1.png In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...** -.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_2.png +.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_2.png The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem): -.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_3.png +.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_3.png But most of the time, the chart will look rather random: -.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png +.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_4.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/maf/interval2maf.xml --- a/tools/maf/interval2maf.xml +++ b/tools/maf/interval2maf.xml @@ -110,7 +110,7 @@ Here a single interval is superimposed on three MAF blocks. Blocks 1 and 3 are trimmed because they extend beyond boundaries of the interval: -.. image:: ./static/images/maf_icons/interval2maf.png +.. image:: ${static_path}/images/maf_icons/interval2maf.png ------- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/maf/interval2maf_pairwise.xml --- a/tools/maf/interval2maf_pairwise.xml +++ b/tools/maf/interval2maf_pairwise.xml @@ -37,7 +37,7 @@ Here a single interval is superimposed on three MAF blocks. Blocks 1 and 3 are trimmed because they extend beyond boundaries of the interval: -.. image:: ./static/images/maf_icons/interval2maf.png +.. image:: ${static_path}/images/maf_icons/interval2maf.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/maf/interval_maf_to_merged_fasta.xml --- a/tools/maf/interval_maf_to_merged_fasta.xml +++ b/tools/maf/interval_maf_to_merged_fasta.xml @@ -101,7 +101,7 @@ Here three MAF blocks overlapping a single interval are stitched together. Space between blocks 2 and 3 is filled with gaps: -.. image:: ./static/images/maf_icons/stitchMaf.png +.. image:: ${static_path}/images/maf_icons/stitchMaf.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/metag_tools/blat_mapping.xml --- a/tools/metag_tools/blat_mapping.xml +++ b/tools/metag_tools/blat_mapping.xml @@ -35,7 +35,7 @@ Showing reads coverage on human chromosome 22 (partial result) in UCSC Genome Browser Custom Track: - .. image:: ./static/images/blat_mapping_example.png + .. image:: ${static_path}/images/blat_mapping_example.png :width: 600 </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/metag_tools/convert_SOLiD_color2nuc.xml --- a/tools/metag_tools/convert_SOLiD_color2nuc.xml +++ b/tools/metag_tools/convert_SOLiD_color2nuc.xml @@ -65,7 +65,7 @@ Each di-nucleotide is represented by a single digit: 0 to 3. The matrix is symmetric, thus the leading nucleotide is necessary to determine the sequence (otherwise there are four possibilities). - .. image:: ./static/images/dualcolorcode.png + .. image:: ${static_path}/images/dualcolorcode.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/metag_tools/short_reads_figure_score.xml --- a/tools/metag_tools/short_reads_figure_score.xml +++ b/tools/metag_tools/short_reads_figure_score.xml @@ -56,7 +56,7 @@ Quality scores are summarized as boxplot (Roche 454 FLX data): -.. image:: ./static/images/short_reads_boxplot.png +.. image:: ${static_path}/images/short_reads_boxplot.png where the **X-axis** is coordinate along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines: diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/mutation/visualize.xml --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -96,7 +96,7 @@ Visualization output: -.. image:: ./static/images/mutation_visualization_example.png +.. image:: ${static_path}/images/mutation_visualization_example.png :width: 150 Here the left-most column represents the position and the background color is the reference base color. Each column on its right describe each sample. diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/basecoverage.xml --- a/tools/new_operations/basecoverage.xml +++ b/tools/new_operations/basecoverage.xml @@ -38,7 +38,7 @@ **Example** -.. image:: ./static/operation_icons/gops_baseCoverage.gif +.. image:: ${static_path}/operation_icons/gops_baseCoverage.gif </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/cluster.xml --- a/tools/new_operations/cluster.xml +++ b/tools/new_operations/cluster.xml @@ -86,11 +86,11 @@ Find Clusters: -.. image:: ./static/operation_icons/gops_clusterFind.gif +.. image:: ${static_path}/operation_icons/gops_clusterFind.gif Merge Clusters: -.. image:: ./static/operation_icons/gops_clusterMerge.gif +.. image:: ${static_path}/operation_icons/gops_clusterMerge.gif </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/complement.xml --- a/tools/new_operations/complement.xml +++ b/tools/new_operations/complement.xml @@ -55,7 +55,7 @@ **Example** -.. image:: ./static/operation_icons/gops_complement.gif +.. image:: ${static_path}/operation_icons/gops_complement.gif </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/concat.xml --- a/tools/new_operations/concat.xml +++ b/tools/new_operations/concat.xml @@ -53,7 +53,7 @@ **Example** -.. image:: ./static/operation_icons/gops_concatenate.gif +.. image:: ${static_path}/operation_icons/gops_concatenate.gif </help></tool> \ No newline at end of file diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/get_flanks.xml --- a/tools/new_operations/get_flanks.xml +++ b/tools/new_operations/get_flanks.xml @@ -58,7 +58,7 @@ chr22 500 800 NM_174568 0 + -.. image:: ./static/operation_icons/flanks_ex1.gif +.. image:: ${static_path}/operation_icons/flanks_ex1.gif **Example 2** @@ -70,7 +70,7 @@ chr22 500 800 NM_028946 0 - -.. image:: ./static/operation_icons/flanks_ex2.gif +.. image:: ${static_path}/operation_icons/flanks_ex2.gif </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/intersect.xml --- a/tools/new_operations/intersect.xml +++ b/tools/new_operations/intersect.xml @@ -133,11 +133,11 @@ Overlapping Intervals: -.. image:: ./static/operation_icons/gops_intersectOverlappingIntervals.gif +.. image:: ${static_path}/operation_icons/gops_intersectOverlappingIntervals.gif Overlapping Pieces of Intervals: -.. image:: ./static/operation_icons/gops_intersectOverlappingPieces.gif +.. image:: ${static_path}/operation_icons/gops_intersectOverlappingPieces.gif </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/join.xml --- a/tools/new_operations/join.xml +++ b/tools/new_operations/join.xml @@ -94,23 +94,23 @@ **Examples** -.. image:: ./static/operation_icons/gops_joinRecordsList.gif +.. image:: ${static_path}/operation_icons/gops_joinRecordsList.gif Only records that are joined (inner join): -.. image:: ./static/operation_icons/gops_joinInner.gif +.. image:: ${static_path}/operation_icons/gops_joinInner.gif All records of first dataset: -.. image:: ./static/operation_icons/gops_joinLeftOuter.gif +.. image:: ${static_path}/operation_icons/gops_joinLeftOuter.gif All records of second dataset: -.. image:: ./static/operation_icons/gops_joinRightOuter.gif +.. image:: ${static_path}/operation_icons/gops_joinRightOuter.gif All records of both datasets: -.. image:: ./static/operation_icons/gops_joinFullOuter.gif +.. image:: ${static_path}/operation_icons/gops_joinFullOuter.gif </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/merge.xml --- a/tools/new_operations/merge.xml +++ b/tools/new_operations/merge.xml @@ -52,7 +52,7 @@ **Example** -.. image:: ./static/operation_icons/gops_merge.gif +.. image:: ${static_path}/operation_icons/gops_merge.gif </help></tool> \ No newline at end of file diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/subtract.xml --- a/tools/new_operations/subtract.xml +++ b/tools/new_operations/subtract.xml @@ -114,11 +114,11 @@ Intervals with no overlap: -.. image:: ./static/operation_icons/gops_subtractOverlappingIntervals.gif +.. image:: ${static_path}/operation_icons/gops_subtractOverlappingIntervals.gif Non-overlapping pieces of intervals: -.. image:: ./static/operation_icons/gops_subtractOverlappingPieces.gif +.. image:: ${static_path}/operation_icons/gops_subtractOverlappingPieces.gif </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/ngs_simulation/ngs_simulation.xml --- a/tools/ngs_simulation/ngs_simulation.xml +++ b/tools/ngs_simulation/ngs_simulation.xml @@ -188,7 +188,7 @@ Plot output (png): -.. image:: ./static/images/ngs_simulation.png +.. image:: ${static_path}/images/ngs_simulation.png Summary output (txt):: diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/beam.xml --- a/tools/phenotype_association/beam.xml +++ b/tools/phenotype_association/beam.xml @@ -59,9 +59,9 @@ The input dataset must be in lped_ format. The output datasets are both tabular_. (`Dataset missing?`_) -.. _lped: ./static/formatHelp.html#lped -.. _tabular: ./static/formatHelp.html#tabular -.. _Dataset missing?: ./static/formatHelp.html +.. _lped: ${static_path}/formatHelp.html#lped +.. _tabular: ${static_path}/formatHelp.html#tabular +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/ctd.xml --- a/tools/phenotype_association/ctd.xml +++ b/tools/phenotype_association/ctd.xml @@ -246,7 +246,7 @@ Home page: http://ctdbase.org -.. _tabular: ./static/formatHelp.html#tab +.. _tabular: ${static_path}/formatHelp.html#tab ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/funDo.xml --- a/tools/phenotype_association/funDo.xml +++ b/tools/phenotype_association/funDo.xml @@ -34,7 +34,7 @@ There is no input dataset. The output is in interval_ format. -.. _interval: ./static/formatHelp.html#interval +.. _interval: ${static_path}/formatHelp.html#interval ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/gpass.xml --- a/tools/phenotype_association/gpass.xml +++ b/tools/phenotype_association/gpass.xml @@ -39,9 +39,9 @@ The input dataset must be in lped_ format, and the output is tabular_. (`Dataset missing?`_) -.. _lped: ./static/formatHelp.html#lped -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _lped: ${static_path}/formatHelp.html#lped +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/hilbertvis.xml --- a/tools/phenotype_association/hilbertvis.xml +++ b/tools/phenotype_association/hilbertvis.xml @@ -63,8 +63,8 @@ The input format is interval_, and the output is an image in PDF format. (`Dataset missing?`_) -.. _interval: ./static/formatHelp.html#interval -.. _Dataset missing?: ./static/formatHelp.html +.. _interval: ${static_path}/formatHelp.html#interval +.. _Dataset missing?: ${static_path}/formatHelp.html ----- @@ -75,7 +75,7 @@ visualization onto a two-dimensional square. For example, here is a diagram showing the path of a level-2 Hilbert curve. -.. image:: ./static/images/hilbertvisDiagram.png +.. image:: ${static_path}/images/hilbertvisDiagram.png The shade of each pixel represents the value for the corresponding bin of consecutive genomic positions, calculated according to the specified @@ -99,11 +99,11 @@ Here are some examples from the HilbertVis homepage, using ChIP-Seq data. -.. image:: ./static/images/hilbertvis1.png +.. image:: ${static_path}/images/hilbertvis1.png ----- -.. image:: ./static/images/hilbertvis2.png +.. image:: ${static_path}/images/hilbertvis2.png ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/ldtools.xml --- a/tools/phenotype_association/ldtools.xml +++ b/tools/phenotype_association/ldtools.xml @@ -34,8 +34,8 @@ The input and output datasets are tabular_. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/linkToDavid.xml --- a/tools/phenotype_association/linkToDavid.xml +++ b/tools/phenotype_association/linkToDavid.xml @@ -76,9 +76,9 @@ a link to the DAVID website as described below. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _html: ./static/formatHelp.html#html -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _html: ${static_path}/formatHelp.html#html +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/linkToGProfile.xml --- a/tools/phenotype_association/linkToGProfile.xml +++ b/tools/phenotype_association/linkToGProfile.xml @@ -48,9 +48,9 @@ The output dataset is html_ with a link to g:Profiler. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _html: ./static/formatHelp.html#html -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _html: ${static_path}/formatHelp.html#html +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/lps.xml --- a/tools/phenotype_association/lps.xml +++ b/tools/phenotype_association/lps.xml @@ -180,9 +180,9 @@ There is a second output dataset (a log) that is in text_ format. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _text: ./static/formatHelp.html#text -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _text: ${static_path}/formatHelp.html#text +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/pass.xml --- a/tools/phenotype_association/pass.xml +++ b/tools/phenotype_association/pass.xml @@ -39,9 +39,9 @@ The input is in GFF_ format, and the output is tabular_. (`Dataset missing?`_) -.. _GFF: ./static/formatHelp.html#gff -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _GFF: ${static_path}/formatHelp.html#gff +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/sift.xml --- a/tools/phenotype_association/sift.xml +++ b/tools/phenotype_association/sift.xml @@ -97,8 +97,8 @@ The input and output datasets are tabular_. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/snpFreq.xml --- a/tools/phenotype_association/snpFreq.xml +++ b/tools/phenotype_association/snpFreq.xml @@ -44,8 +44,8 @@ and includes all of the input data plus the additional columns described below. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/plotting/bar_chart.xml --- a/tools/plotting/bar_chart.xml +++ b/tools/plotting/bar_chart.xml @@ -52,7 +52,7 @@ Graphing columns 2 and 3 while using column 1 for X Tick Labels will produce the following plot: -.. image:: ./static/images/bar_chart.png +.. image:: ${static_path}/images/bar_chart.png :height: 324 :width: 540 diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/plotting/boxplot.xml --- a/tools/plotting/boxplot.xml +++ b/tools/plotting/boxplot.xml @@ -95,7 +95,7 @@ * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1) * Whiskers show outliers at max. 1.5*IQR -.. image:: ./static/images/solid_qual.png +.. image:: ${static_path}/images/solid_qual.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/plotting/histogram2.xml --- a/tools/plotting/histogram2.xml +++ b/tools/plotting/histogram2.xml @@ -70,7 +70,7 @@ - Create a histogram on column 2 of the above dataset. -.. image:: ./static/images/histogram2.png +.. image:: ${static_path}/images/histogram2.png </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/plotting/scatterplot.xml --- a/tools/plotting/scatterplot.xml +++ b/tools/plotting/scatterplot.xml @@ -65,7 +65,7 @@ - Create a simple scatterplot between the variables in column 2 and column 3 of the above dataset. -.. image:: ./static/images/scatterplot.png +.. image:: ${static_path}/images/scatterplot.png </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/plotting/xy_plot.xml --- a/tools/plotting/xy_plot.xml +++ b/tools/plotting/xy_plot.xml @@ -143,6 +143,6 @@ - Series 1: Red Dashed-Line plot between columns 1 and 2 - Series 2: Blue Circular-Point plot between columns 3 and 2 -.. image:: ./static/images/xy_example.jpg +.. image:: ${static_path}/images/xy_example.jpg </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/regVariation/compute_q_values.xml --- a/tools/regVariation/compute_q_values.xml +++ b/tools/regVariation/compute_q_values.xml @@ -141,13 +141,13 @@ 0.03115264 0.009750824 1 -.. image:: ./static/operation_icons/p_hist.png +.. image:: ${static_path}/operation_icons/p_hist.png -.. image:: ./static/operation_icons/q_hist.png +.. image:: ${static_path}/operation_icons/q_hist.png -.. image:: ./static/operation_icons/Q_plots.png +.. image:: ${static_path}/operation_icons/Q_plots.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/regVariation/draw_stacked_barplots.xml --- a/tools/regVariation/draw_stacked_barplots.xml +++ b/tools/regVariation/draw_stacked_barplots.xml @@ -52,7 +52,7 @@ The stacked bars plot representing the data in the input file. -.. image:: ./static/operation_icons/stacked_bars_plot.png +.. image:: ${static_path}/operation_icons/stacked_bars_plot.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/rgenetics/rgManQQ.xml --- a/tools/rgenetics/rgManQQ.xml +++ b/tools/rgenetics/rgManQQ.xml @@ -86,7 +86,7 @@ improbable p values are above the red line which is drawn at the Bonferroni FWER control level (0.05/n where n is the number of tests - this is highly conservative for correlated SNPs typical of GWA) -.. image:: ./static/images/Armitagep_manhattan.png +.. image:: ${static_path}/images/Armitagep_manhattan.png A quantile-quantile (QQ) plot is a good way to see systematic departures from the null expectation of uniform p-values from a genomic analysis. If the QQ plot shows departure from the null (ie a uniform 0-1 @@ -94,7 +94,7 @@ interesting results to look at. A log scale will help emphasise departures from the null at low p values more clear -.. image:: ./static/images/Armitagep_qqplot.png +.. image:: ${static_path}/images/Armitagep_qqplot.png ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/rgenetics/rgWebLogo3.xml --- a/tools/rgenetics/rgWebLogo3.xml +++ b/tools/rgenetics/rgWebLogo3.xml @@ -106,7 +106,7 @@ A typical output looks like this -.. image:: ./static/images/rgWebLogo3_test.jpg +.. image:: ${static_path}/images/rgWebLogo3_test.jpg ---- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml +++ b/tools/samtools/pileup_parser.xml @@ -320,7 +320,7 @@ To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows: -.. image:: ./static/images/pileup_parser_help1.png +.. image:: ${static_path}/images/pileup_parser_help1.png Running the tool with these parameters will return:: @@ -336,7 +336,7 @@ In addition to calling variants, it is often useful to know the quality adjusted coverage. Running the tool with these parameters: -.. image:: ./static/images/pileup_parser_help2.png +.. image:: ${static_path}/images/pileup_parser_help2.png will report everything from the original file:: @@ -355,7 +355,7 @@ If you set the **Print total number of differences?** to **Yes** the tool will print an additional column with the total number of reads where a devinat base is above the quality threshold. So, seetiing parametrs like this: -.. image:: ./static/images/pileup_parser_help3.png +.. image:: ${static_path}/images/pileup_parser_help3.png will produce this:: @@ -371,7 +371,7 @@ Setting **Print quality and base string?** to **Yes** as shown here: -.. image:: ./static/images/pileup_parser_help4.png +.. image:: ${static_path}/images/pileup_parser_help4.png will produce this:: diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/solid_tools/solid_qual_boxplot.xml --- a/tools/solid_tools/solid_qual_boxplot.xml +++ b/tools/solid_tools/solid_qual_boxplot.xml @@ -29,7 +29,7 @@ * Whiskers show outliers at max. 1.5*IQR -.. image:: ./static/images/solid_qual.png +.. image:: ${static_path}/images/solid_qual.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/stats/cor.xml --- a/tools/stats/cor.xml +++ b/tools/stats/cor.xml @@ -47,19 +47,19 @@ - **Pearson's Correlation** reflects the degree of linear relationship between two variables. It ranges from +1 to -1. A correlation of +1 means that there is a perfect positive linear relationship between variables. The formula for Pearson's correlation is: - .. image:: ./static/images/pearson.png + .. image:: ${static_path}/images/pearson.png where n is the number of items - **Kendall's rank correlation** is used to measure the degree of correspondence between two rankings and assessing the significance of this correspondence. The formula for Kendall's rank correlation is: - .. image:: ./static/images/kendall.png + .. image:: ${static_path}/images/kendall.png where n is the number of items, and P is the sum. - **Spearman's rank correlation** assesses how well an arbitrary monotonic function could describe the relationship between two variables, without making any assumptions about the frequency distribution of the variables. The formula for Spearman's rank correlation is - .. image:: ./static/images/spearman.png + .. image:: ${static_path}/images/spearman.png where D is the difference between the ranks of corresponding values of X and Y, and N is the number of pairs of values. diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/stats/generate_matrix_for_pca_lda.xml --- a/tools/stats/generate_matrix_for_pca_lda.xml +++ b/tools/stats/generate_matrix_for_pca_lda.xml @@ -35,12 +35,12 @@ - Input file (Source file First) -.. image:: ./static/images/tools/lda/first_matrix_generator_example_file.png +.. image:: ${static_path}/images/tools/lda/first_matrix_generator_example_file.png - Input file (Source file Second) -.. image:: ./static/images/tools/lda/second_matrix_generator_example_file.png +.. image:: ${static_path}/images/tools/lda/second_matrix_generator_example_file.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/taxonomy/gi2taxonomy.xml --- a/tools/taxonomy/gi2taxonomy.xml +++ b/tools/taxonomy/gi2taxonomy.xml @@ -50,7 +50,7 @@ and you want to obtain full taxonomic representation for GIs listed in *targetGI* column. If you set parameters as shown here: -.. image:: ./static/images/fetchTax.png +.. image:: ${static_path}/images/fetchTax.png the tool will generate the following output (you may need to scroll sideways to see the entire line):: diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/taxonomy/poisson2test.xml --- a/tools/taxonomy/poisson2test.xml +++ b/tools/taxonomy/poisson2test.xml @@ -48,12 +48,12 @@ Equation 1: -.. image:: ./static/images/poisson2test_eqn1.png +.. image:: ${static_path}/images/poisson2test_eqn1.png Equation 2: -.. image:: ./static/images/poisson2test_eqn2.png +.. image:: ${static_path}/images/poisson2test_eqn2.png X = number of reads falling in a particular taxon in location 1 diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/taxonomy/t2ps_wrapper.xml --- a/tools/taxonomy/t2ps_wrapper.xml +++ b/tools/taxonomy/t2ps_wrapper.xml @@ -62,14 +62,14 @@ Drawing the tree with default parameters (without changing anything in the interface) will produce this tree: -.. image:: ./static/images/t2ps_ideal.png +.. image:: ${static_path}/images/t2ps_ideal.png :width: 500 (for explanation of colors and numbers on the tree scroll to the bottom of this help section) Here *Class* rank represent terminal nodes (leaves) of the tree because it is the default setting of the "*show ranks from root to*" drop-down. Changing the drop-down to "*Subspecies*" will produce this: -.. image:: ./static/images/t2ps_ideal_ssp.png +.. image:: ${static_path}/images/t2ps_ideal_ssp.png :width: 1000 -------- @@ -87,7 +87,7 @@ A full tree for this dataset will look like this: -.. image:: ./static/images/t2ps_missing_nodes.png +.. image:: ${static_path}/images/t2ps_missing_nodes.png :width: 1000 Missing nodes are simply omitted from the tree (there are no gray boxes corresponding to "n") but the branch length is maintained so that taxa belonging to the same taxonomic rank are always aligned with each other @@ -98,11 +98,11 @@ You can use the "*maximum number of leaves*" to restrict the tree to a specified number of leaves (external nodes). Using the following setting on the above dataset (note *show ranks from root to* set to *show entire tree* and *maximum number of leaves* is set *3*): -.. image:: ./static/images/t2ps_autoscale.png +.. image:: ${static_path}/images/t2ps_autoscale.png will produce this tree: -.. image:: ./static/images/t2ps_autoscale_tree.png +.. image:: ${static_path}/images/t2ps_autoscale_tree.png :width: 1000 Here the tree is automatically trimmed at a taxonomic rank that will only have 3 outer nodes. This is very useful for initial evaluation of very large trees where you want to only see, say, 1,000 outer nodes at once. @@ -113,11 +113,11 @@ Branches of the tree are colored according to the heatmap below. The "bluer" the branch the lesser the number of leaves it leads to and vice versa. -.. image:: ./static/images/t2ps_heatmap.png +.. image:: ${static_path}/images/t2ps_heatmap.png Each node is labeled with taxonomic name and the number of tree leaves belonging to this taxonomic group: -.. image:: ./static/images/t2ps_node_label.png +.. image:: ${static_path}/images/t2ps_node_label.png Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.