1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/863fc12ce692/ changeset: r5539:863fc12ce692 user: kellyv date: 2011-05-11 16:49:32 summary: Updated SRMA to properly set dbkey and changed functional tests so that they can handle a single line difference for the SRMA version number tag affected #: 2 files (1.5 KB)

--- a/tools/sr_mapping/srma_wrapper.py Wed May 11 10:46:46 2011 -0400 +++ b/tools/sr_mapping/srma_wrapper.py Wed May 11 10:49:32 2011 -0400 @@ -3,23 +3,10 @@ """ Runs SRMA on a SAM/BAM file; TODO: more documentation -TODO: Allow use of fastq file in user's history, will need to index on-the-fly

usage: srma_wrapper.py [options] - -r, --ref=r: The reference genome to use or index - -i, --input=i: The SAM/BAM input file - -o, --output=o: The SAM/BAM output file - -O, --offset=O: The alignment offset - -Q, --minMappingQuality=Q: The minimum mapping quality - -P, --minAlleleProbability=P: The minimum allele probability conditioned on coverage (for the binomial quantile). - -C, --minAlleleCoverage=C: The minimum haploid coverage for the consensus. Default value: 3. This option can be set - -R, --range=R: A range to examine - -c, --correctBases=c: Correct bases - -q, --useSequenceQualities=q: Use sequence qualities - -M, --maxHeapSize=M: The maximum number of nodes on the heap before re-alignment is ignored - -s, --fileSource=s: Whether to use a previously indexed reference sequence or one from history (indexed or history) - -p, --params=p: Parameter setting to use (pre_set or full) - -D, --dbkey=D: Dbkey for reference genome + +See below for options """

import optparse, os, shutil, subprocess, sys, tempfile

--- a/tools/sr_mapping/srma_wrapper.xml Wed May 11 10:46:46 2011 -0400 +++ b/tools/sr_mapping/srma_wrapper.xml Wed May 11 10:49:32 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="srma_wrapper" name="Re-align with SRMA" version="0.2.1"> +<tool id="srma_wrapper" name="Re-align with SRMA" version="0.2.5"><description></description><command interpreter="python">srma_wrapper.py #if $refGenomeSource.refGenomeSource_type == "history": @@ -34,7 +34,10 @@ </param><when value="built-in"><param name="ref" type="select" label="Select a reference genome"> - <options from_data_table="srma_indexes" /> + <options from_data_table="srma_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options></param></when><when value="history"> @@ -66,12 +69,17 @@ <conditional name="refGenomeSource.refGenomeSource_type"><when value="built-in"><action type="metadata" name="dbkey"> - <option type="from_file" name="srma_index.loc" column="0" offset="0"> + <option type="from_data_table" name="srma_indexes" column="1" offset="0"><filter type="param_value" column="0" value="#" compare="startswith" keep="False" /> - <filter type="param_value" ref="refGenomeSource.ref" column="1" /> + <filter type="param_value" ref="refGenomeSource.ref" column="0" /></option></action></when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when></conditional></actions></data> @@ -91,7 +99,7 @@ <param name="ref" value="hg18chr21" /><param name="input" value="srma_in1.bam" type="bam" /><param name="source_select" value="pre_set" /> - <output name="output" file="srma_out1.bam" ftype="bam"/> + <output name="output" file="srma_out1.bam" ftype="bam" lines_diff="2" /><!-- allows tag with version number to be different --></test><test><!-- Commands to run to prepare test files (uses custom genome): @@ -107,8 +115,8 @@ samtools sort srma_in3.u.bam srma_in3 --><param name="refGenomeSource_type" value="history" /> - <param name="ownFile" value="srma_in2.fa" /> - <param name="input" value="srma_in3.bam" type="bam" /> + <param name="ownFile" value="srma_in2.fa" ftype="fasta" /> + <param name="input" value="srma_in3.bam" ftype="bam" /><param name="source_select" value="full" /><param name="offset" value="20" /><param name="minMappingQuality" value="0" /> @@ -118,7 +126,7 @@ <param name="correctBases" value="true" /><param name="useSequenceQualities" value="true" /><param name="maxHeapSize" value="8192" /> - <output name="output" file="srma_out2.bam" ftype="bam"/> + <output name="output" file="srma_out2.bam" ftype="bam" lines_diff="2" /><!-- allows tag with version number to be different --></test></tests><help>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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