Mercurial > repos > pjbriggs > ceas
diff ceas_wrapper.xml @ 10:b5d686bb9d6f draft
Version 1.0.2-3: get dependencies from conda.
author | pjbriggs |
---|---|
date | Wed, 28 Feb 2018 06:04:06 -0500 |
parents | 4c3b7130dbbb |
children | d3bd9caee1b7 |
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--- a/ceas_wrapper.xml Tue Oct 18 09:24:30 2016 -0400 +++ b/ceas_wrapper.xml Wed Feb 28 06:04:06 2018 -0500 @@ -1,14 +1,12 @@ <tool id="ceas" name="CEAS" version="1.0.2-3"> <description>Annotate intervals and scores with genome features</description> <requirements> - <requirement type="package" version="1.2.5">python_mysqldb</requirement> - <requirement type="package" version="0.7.1">bx-python</requirement> - <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement> - <requirement type="package" version="1.0">ucsc_fetchChromSizes</requirement> - <requirement type="package" version="3.1.2">R</requirement> + <requirement type="package" version="1.0.2b1">cistrome-ceas</requirement> + <requirement type="package" version="357">ucsc-fetchchromsizes</requirement> </requirements> <version_command>ceas --version 2>&1 | tail -1</version_command> - <command interpreter="bash">ceas_wrapper.sh + <command><![CDATA[ + bash $__tool_directory__/ceas_wrapper.sh $bed_file ${gdb_file.fields.path} $log_output $pdf_report $xls_output #if (str($wig_file) != 'None') @@ -28,7 +26,8 @@ --sizes $sizes_lower,$sizes_middle,$sizes_upper --bisizes $bisizes_lower,$bisizes_upper --pf-res $profiling_resolution - --rel-dist $relative_distance</command> + --rel-dist $relative_distance + ]]></command> <inputs> <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" /> <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true"