commit/galaxy-central: 4 new changesets
4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/882d74715634/ Changeset: 882d74715634 Branch: ccat3 User: BjoernGruening Date: 2013-11-11 10:09:54 Summary: add dependency of type package to the ccat wrapper Affected #: 1 file diff -r ea6ff3d7224db5d218eefa91af1b08626229eae1 -r 882d7471563422315959211baf12e89ae0e94a29 tools/peak_calling/ccat_wrapper.xml --- a/tools/peak_calling/ccat_wrapper.xml +++ b/tools/peak_calling/ccat_wrapper.xml @@ -10,6 +10,7 @@ '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command><requirements><requirement type="binary" version="3.0">CCAT</requirement> + <requirement type="package" version="3.0">CCAT</requirement></requirements><inputs><param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > https://bitbucket.org/galaxy/galaxy-central/commits/446d410097fd/ Changeset: 446d410097fd Branch: ccat3 User: BjoernGruening Date: 2013-11-11 10:10:41 Summary: remove ccat_2_wrapper.xml, afaik it is not used anymore Affected #: 1 file diff -r 882d7471563422315959211baf12e89ae0e94a29 -r 446d410097fd99711d3ef3160f8fd4e74f9d1a94 tools/peak_calling/ccat_2_wrapper.xml --- a/tools/peak_calling/ccat_2_wrapper.xml +++ /dev/null @@ -1,130 +0,0 @@ -<tool id="peakcalling_ccat2" name="CCAT" version="0.0.1"> - <description>Control-based ChIP-seq Analysis Tool</description> - <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' - #if str( $options_type[ 'options_type_selector' ] ) == 'advanced': - '$input_advanced_config_file' - #else: - '${ options_type.input_config_file.fields.path }' - #end if - 'CCAT in Galaxy' - '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command> - <requirements> - <requirement type="binary">CCAT</requirement> - </requirements> - <inputs> - <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > - <validator type="unspecified_build" /> - </param> - <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" > - <validator type="unspecified_build" /> - </param> - <conditional name="options_type"> - <param name="options_type_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic"> - <param name="input_config_file" type="select" label="Select a pre-defined configuration file"> - <options from_data_table="ccat_configurations"> - <validator type="no_options" message="No configurations are available"/> - </options> - </param> - </when> - <when value="advanced"> - <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/> - <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/> - <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/> - <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" > - <option value="1">Transition from sense strand to anti-sense strand</option> - <option value="0" selected="True">Local maximum of read-enrichment profile</option> - </param> - <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/> - <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/> - <param name="random_seed" type="integer" label="Random Seed" value="123456"/> - <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/> - <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> - </outputs> - <configfiles> - <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced': -fragmentSize ${options_type[ 'fragment_size' ]} -slidingWinSize ${options_type[ 'sliding_window_size' ]} -movingStep ${options_type[ 'moving_step' ]} -isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]} -minCount ${options_type[ 'min_count' ]} -outputNum ${options_type[ 'output_num' ]} -randomSeed ${options_type[ 'random_seed' ]} -minScore ${options_type[ 'min_score' ]} -bootstrapPass ${options_type[ 'bootstrap_pass' ]} -#end if</configfile> - </configfiles> - <tests> - <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="options_type_selector" value="basic" /> - <param name="input_config_file" value="ccat_2.0_histone_config" /> - <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> - <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> - <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> - <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> - </test> - <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="options_type_selector" value="advanced" /> - <param name="fragment_size" value="200" /> - <param name="sliding_window_size" value="500" /> - <param name="moving_step" value="50" /> - <param name="is_strand_sensitive_mode" value="0" /> - <param name="min_count" value="4" /> - <param name="output_num" value="100000" /> - <param name="random_seed" value="123456" /> - <param name="min_score" value="3.0" /> - <param name="bootstrap_pass" value="50" /> - <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> - <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> - <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> - <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> - </test> - </tests> - <help> -**What it does** - -This tool allows ChIP-seq peak/region calling using CCAT. - -View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. - ------- - -**Citation** - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - - </help> -</tool> https://bitbucket.org/galaxy/galaxy-central/commits/936b96845324/ Changeset: 936b96845324 Branch: ccat3 User: BjoernGruening Date: 2013-11-11 15:35:45 Summary: remove binary dependency Affected #: 1 file diff -r 446d410097fd99711d3ef3160f8fd4e74f9d1a94 -r 936b96845324311668e5ee82761ed18a551a9fa1 tools/peak_calling/ccat_wrapper.xml --- a/tools/peak_calling/ccat_wrapper.xml +++ b/tools/peak_calling/ccat_wrapper.xml @@ -9,7 +9,6 @@ 'CCAT in Galaxy' '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command><requirements> - <requirement type="binary" version="3.0">CCAT</requirement><requirement type="package" version="3.0">CCAT</requirement></requirements><inputs> https://bitbucket.org/galaxy/galaxy-central/commits/0fb6c5d7312a/ Changeset: 0fb6c5d7312a User: natefoo Date: 2013-12-20 16:23:16 Summary: Merged in BjoernGruening/galaxy-central-bgruening/ccat3 (pull request #257) Adding requirement tag to the ccat wrapper and remove old ccat2 wrapper. Affected #: 1 file diff -r 2fcb2c12183df5ee7ec96d0f1a253c23448e4410 -r 0fb6c5d7312aafece427c4e9b19dc5e5b991c6d8 tools/peak_calling/ccat_2_wrapper.xml --- a/tools/peak_calling/ccat_2_wrapper.xml +++ /dev/null @@ -1,130 +0,0 @@ -<tool id="peakcalling_ccat2" name="CCAT" version="0.0.1"> - <description>Control-based ChIP-seq Analysis Tool</description> - <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' - #if str( $options_type[ 'options_type_selector' ] ) == 'advanced': - '$input_advanced_config_file' - #else: - '${ options_type.input_config_file.fields.path }' - #end if - 'CCAT in Galaxy' - '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command> - <requirements> - <requirement type="binary">CCAT</requirement> - </requirements> - <inputs> - <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > - <validator type="unspecified_build" /> - </param> - <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" > - <validator type="unspecified_build" /> - </param> - <conditional name="options_type"> - <param name="options_type_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic"> - <param name="input_config_file" type="select" label="Select a pre-defined configuration file"> - <options from_data_table="ccat_configurations"> - <validator type="no_options" message="No configurations are available"/> - </options> - </param> - </when> - <when value="advanced"> - <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/> - <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/> - <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/> - <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" > - <option value="1">Transition from sense strand to anti-sense strand</option> - <option value="0" selected="True">Local maximum of read-enrichment profile</option> - </param> - <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/> - <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/> - <param name="random_seed" type="integer" label="Random Seed" value="123456"/> - <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/> - <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> - </outputs> - <configfiles> - <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced': -fragmentSize ${options_type[ 'fragment_size' ]} -slidingWinSize ${options_type[ 'sliding_window_size' ]} -movingStep ${options_type[ 'moving_step' ]} -isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]} -minCount ${options_type[ 'min_count' ]} -outputNum ${options_type[ 'output_num' ]} -randomSeed ${options_type[ 'random_seed' ]} -minScore ${options_type[ 'min_score' ]} -bootstrapPass ${options_type[ 'bootstrap_pass' ]} -#end if</configfile> - </configfiles> - <tests> - <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="options_type_selector" value="basic" /> - <param name="input_config_file" value="ccat_2.0_histone_config" /> - <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> - <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> - <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> - <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> - </test> - <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="options_type_selector" value="advanced" /> - <param name="fragment_size" value="200" /> - <param name="sliding_window_size" value="500" /> - <param name="moving_step" value="50" /> - <param name="is_strand_sensitive_mode" value="0" /> - <param name="min_count" value="4" /> - <param name="output_num" value="100000" /> - <param name="random_seed" value="123456" /> - <param name="min_score" value="3.0" /> - <param name="bootstrap_pass" value="50" /> - <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> - <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> - <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> - <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> - </test> - </tests> - <help> -**What it does** - -This tool allows ChIP-seq peak/region calling using CCAT. - -View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. - ------- - -**Citation** - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - - </help> -</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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