Mercurial > repos > devteam > cuffdiff
diff cuffdiff_wrapper.xml @ 3:9ec1cc10742c draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author | devteam |
---|---|
date | Tue, 07 Feb 2017 18:38:03 -0500 (2017-02-07) |
parents | c139f0dd4ee6 |
children | e20b05db0839 |
line wrap: on
line diff
--- a/cuffdiff_wrapper.xml Thu Oct 29 22:33:47 2015 -0400 +++ b/cuffdiff_wrapper.xml Tue Feb 07 18:38:03 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" />