| Previous changeset 12:0f32ad418df8 (2015-11-11) Next changeset 14:d3ae7d9c2202 (2017-02-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f |
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modified:
cuff_macros.xml cuffdiff_wrapper.xml tool_dependencies.xml |
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| diff -r 0f32ad418df8 -r f1b92120dfaa cuff_macros.xml --- a/cuff_macros.xml Wed Nov 11 12:34:34 2015 -0500 +++ b/cuff_macros.xml Tue Feb 07 18:39:02 2017 -0500 |
| [ |
| @@ -1,11 +1,13 @@ <macros> <token name="@VERSION@">2.2.1</token> + <xml name="requirements"> <requirements> <requirement type="package" version="2.2.1">cufflinks</requirement> <yield /> </requirements> </xml> + <xml name="stdio"> <stdio> <exit_code range="1:" /> @@ -26,21 +28,21 @@ </param> <when value="BAM"> <repeat name="conditions" title="Condition" min="2"> - <param name="name" title="Condition name" type="text" label="Name"/> + <param name="name" label="Condition name" type="text"/> <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> </repeat> </when> <when value="CXB"> <repeat name="conditions" title="Condition" min="2"> - <param name="name" title="Condition name" type="text" label="Name"/> + <param name="name" label="Condition name" type="text"/> <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> </repeat> </when> <when value="CONDITION_LIST"> - <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list" /> + <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" /> </when> <when value="CONDITION_REPLICATE_LIST"> - <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" /> + <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" /> </when> </conditional> </xml> @@ -48,16 +50,16 @@ #if $in_type.set_in_type in ['BAM', 'CXB'] #for $condition in $in_type.conditions: #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) - $samples + '$samples' #end for #elif $in_type.set_in_type == 'CONDITION_LIST' #for $sample in $in_type.conditions: - $sample + '$sample' #end for #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' #for $condition_list in $in_type.conditions: #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) - $samples + '$samples' #end for #end if </token> @@ -79,11 +81,11 @@ <token name="@CUFFLINKS_GTF_INPUTS@"> ## Inputs. #for $input_file in $inputs: - "${input_file}" + '${input_file}' #end for #for $additional_input in $additional_inputs: #for $input_file in $additional_input.additional_inputs: - "${input_file}" + '${input_file}' #end for #end for </token> |
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| diff -r 0f32ad418df8 -r f1b92120dfaa cuffdiff_wrapper.xml --- a/cuffdiff_wrapper.xml Wed Nov 11 12:34:34 2015 -0500 +++ b/cuffdiff_wrapper.xml Tue Feb 07 18:39:02 2017 -0500 |
| [ |
| @@ -1,14 +1,12 @@ -<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.3"> +<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.4"> <description>find significant changes in transcript expression, splicing, and promoter use</description> - <requirements> - <requirement type="set_environment">CUFFDIFF_SCRIPT_PATH</requirement> - <requirement type="package" version="2.2.1">cufflinks</requirement> - <requirement type="package" version="2.8.2">cummeRbund</requirement> - </requirements> - <expand macro="stdio" /> <macros> <import>cuff_macros.xml</import> </macros> + <expand macro="requirements"> + <requirement type="package" version="2.8.2">bioconductor-cummerbund</requirement> + </expand> + <expand macro="stdio" /> <version_command>cuffdiff 2>&1 | head -n 1</version_command> <command><![CDATA[ cuffdiff @@ -36,10 +34,10 @@ -b #if $bias_correction.seq_source.index_source == "history": ## Custom genome from history. - $bias_correction.seq_source.ref_file + '$bias_correction.seq_source.ref_file' #else: ## Built-in genome. - "${ bias_correction.seq_source.index.fields.path }" + '${bias_correction.seq_source.index.fields.path}' #end if #end if @@ -53,7 +51,7 @@ --library-type=$advanced_settings.library_type #end if #if $advanced_settings.mask_file: - --mask-file=$advanced_settings.mask_file + --mask-file '$advanced_settings.mask_file' #end if #if $advanced_settings.time_series: --time-series @@ -66,12 +64,12 @@ --min-reps-for-js-test=$advanced_settings.min_reps_for_js_test #end if ## Inputs. - $gtf_input + '$gtf_input' @CONDITION_SAMPLES@ #if $generate_sqlite: && - R --vanilla --no-save -f \$CUFFDIFF_SCRIPT_PATH/cummeRbund.R && mv cummeRbund.sqlite "${output_cummerbund}" + R --vanilla --no-save -f '$__tool_directory__/cummeRbund.R' && mv cummeRbund.sqlite '${output_cummerbund}' #end if ]]> </command> @@ -276,15 +274,11 @@ <param name="set_in_type" value="BAM" /> <repeat name="conditions"> <param name="name" value="q1" /> - <repeat name="samples"> - <param name="sample" value="cuffdiff_in1.sam" ftype="sam" /> - </repeat> + <param name="samples" value="cuffdiff_in1.sam" ftype="sam" /> </repeat> <repeat name="conditions"> <param name="name" value="q2" /> - <repeat name="samples"> - <param name="sample" value="cuffdiff_in2.sam" ftype="sam" /> - </repeat> + <param name="samples" value="cuffdiff_in2.sam" ftype="sam" /> </repeat> </conditional> <param name="fdr" value="0.05" /> @@ -293,7 +287,7 @@ <param name="do_normalization" value="No" /> <param name="multiread_correct" value="No"/> <param name="sAdditional" value="No"/> - <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite"/> + <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" /> </test> <test> <!-- @@ -305,15 +299,11 @@ <param name="set_in_type" value="BAM" /> <repeat name="conditions"> <param name="name" value="q1" /> - <repeat name="samples"> - <param name="sample" value="cuffdiff_in1.sam" ftype="sam" /> - </repeat> + <param name="samples" value="cuffdiff_in1.sam" ftype="sam" /> </repeat> <repeat name="conditions"> <param name="name" value="q2" /> - <repeat name="samples"> - <param name="sample" value="cuffdiff_in2.sam" ftype="sam" /> - </repeat> + <param name="samples" value="cuffdiff_in2.sam" ftype="sam" /> </repeat> </conditional> <param name="fdr" value="0.05" /> |
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| diff -r 0f32ad418df8 -r f1b92120dfaa tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 11 12:34:34 2015 -0500 +++ b/tool_dependencies.xml Tue Feb 07 18:39:02 2017 -0500 |
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| @@ -7,6 +7,6 @@ <repository changeset_revision="899067a260d1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="cummeRbund" version="2.8.2"> - <repository changeset_revision="13c270433440" name="package_cummerbund_2_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="754912f24120" name="package_cummerbund_2_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |