Mercurial > repos > nilesh > rseqc
diff inner_distance.xml @ 13:a7f9084572fe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
| author | iuc |
|---|---|
| date | Sat, 10 Dec 2022 11:21:47 +0000 |
| parents | 57fad5deeb8e |
| children |
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--- a/inner_distance.xml Sat Dec 18 19:40:16 2021 +0000 +++ b/inner_distance.xml Sat Dec 10 11:21:47 2022 +0000 @@ -1,10 +1,11 @@ -<tool id="rseqc_inner_distance" name="Inner Distance" version="@TOOL_VERSION@.1"> +<tool id="rseqc_inner_distance" name="Inner Distance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>calculate the inner distance (or insert size) between two paired RNA reads</description> - <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> + <expand macro="bio_tools"/> + <expand macro="requirements" /> <expand macro="stdio" /> @@ -12,7 +13,8 @@ <version_command><![CDATA[inner_distance.py --version]]></version_command> <command><![CDATA[ - inner_distance.py -i '${input}' -o output -r '${refgene}' + @BAM_SAM_INPUTS@ + inner_distance.py -i 'input.${extension}' -o output -r '${refgene}' --sample-size ${sample_size} --lower-bound ${lowerBound} --upper-bound ${upperBound} @@ -33,10 +35,10 @@ </inputs> <outputs> - <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" /> - <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string} (text)"/> - <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string} (frequency text)" /> - <expand macro="rscript_output_data" filename="output.inner_distance_plot.r" /> + <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/> + <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string}: TXT"/> + <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string}: frequency (TXT)" /> + <expand macro="rscript_output_data" filename="output.inner_distance_plot.r" label="${tool.name} on ${on_string}: Rscript"/> </outputs> <tests>