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comparison ceas_wrapper.xml @ 3:df54f8fcc7a7 draft

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Version 1.0.2-3: move to conda-based dependency resolution.
author pjbriggs
date Wed, 28 Feb 2018 10:22:32 -0500
parents d2283cca00cd
children cd6a48ffd093
comparison
equal deleted inserted replaced
2:d2283cca00cd 3:df54f8fcc7a7
1 <tool id="ceas" name="CEAS" version="1.0.2-3"> 1 <tool id="ceas" name="CEAS" version="1.0.2-3">
2 <description>Annotate intervals and scores with genome features</description> 2 <description>Annotate intervals and scores with genome features</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.5">python_mysqldb</requirement> 4 <requirement type="package" version="1.0.2b1">cistrome-ceas</requirement>
5 <requirement type="package" version="0.7.1">bx-python</requirement> 5 <requirement type="package" version="357">ucsc-fetchchromsizes</requirement>
6 <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
7 <requirement type="package" version="1.0">ucsc_fetchChromSizes</requirement>
8 <requirement type="package" version="3.1.2">R</requirement>
9 </requirements> 6 </requirements>
10 <version_command>ceas --version 2&gt;&amp;1 | tail -1</version_command> 7 <version_command>ceas --version 2&gt;&amp;1 | tail -1</version_command>
11 <command interpreter="bash">ceas_wrapper.sh 8 <command><![CDATA[
9 bash $__tool_directory__/ceas_wrapper.sh
12 $bed_file ${gdb_file.fields.path} 10 $bed_file ${gdb_file.fields.path}
13 $log_output $pdf_report $xls_output 11 $log_output $pdf_report $xls_output
14 #if (str($wig_file) != 'None') 12 #if (str($wig_file) != 'None')
15 #if (str($wig_file.ext) == 'bigwig') 13 #if (str($wig_file.ext) == 'bigwig')
16 --bigwig $wig_file 14 --bigwig $wig_file
26 --span $span 24 --span $span
27 #end if 25 #end if
28 --sizes $sizes_lower,$sizes_middle,$sizes_upper 26 --sizes $sizes_lower,$sizes_middle,$sizes_upper
29 --bisizes $bisizes_lower,$bisizes_upper 27 --bisizes $bisizes_lower,$bisizes_upper
30 --pf-res $profiling_resolution 28 --pf-res $profiling_resolution
31 --rel-dist $relative_distance</command> 29 --rel-dist $relative_distance
30 ]]></command>
32 <inputs> 31 <inputs>
33 <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" /> 32 <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" />
34 <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true" 33 <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true"
35 help="If not supplied then only perform ChIP region annotation and gene-centered annotation" /> 34 help="If not supplied then only perform ChIP region annotation and gene-centered annotation" />
36 <param name="extra_bed_file" type="data" format="bed" label="BED file with extra regions of interest (e.g. non-coding regions)" optional="true" /> 35 <param name="extra_bed_file" type="data" format="bed" label="BED file with extra regions of interest (e.g. non-coding regions)" optional="true" />