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comparison merge_pcr_duplicates.xml @ 55:4bedd35bcdff draft

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Move deps from macros to individual tools
author rnateam
date Fri, 12 Feb 2016 08:37:33 -0500
parents c112f77f0466
children b0d5cd8e4c6b
comparison
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54:7a05b21c5629 55:4bedd35bcdff
1 <tool id="merge_pcr_duplicates.py" name="Merge PCR duplicates" version="0.2.0"> 1 <tool id="merge_pcr_duplicates.py" name="Merge PCR duplicates" version="0.2.0">
2 <description>according to random barcode library.</description> 2 <description>according to random barcode library.</description>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="4.1.0">gnu_awk</requirement>
6 <requirement type="package" version="8.22">gnu_coreutils</requirement>
7 <requirement type="package" version="1.0.6">datamash</requirement>
8 </requirements>
9 </xml>
3 <macros> 10 <macros>
4 <import>macros.xml</import> 11 <import>macros.xml</import>
5 </macros> 12 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" /> 13 <expand macro="stdio" />
8 <version_command>python $__tool_directory__/merge_pcr_duplicates.py --version</version_command> 14 <version_command>python $__tool_directory__/merge_pcr_duplicates.py --version</version_command>
9 <command interpreter="python"><![CDATA[merge_pcr_duplicates.py 15 <command interpreter="python"><![CDATA[merge_pcr_duplicates.py
10 #if $positional_1 and $positional_1 is not None: 16 #if $positional_1 and $positional_1 is not None:
11 $positional_1 17 $positional_1
13 19
14 #if $positional_2 and $positional_2 is not None: 20 #if $positional_2 and $positional_2 is not None:
15 $positional_2 21 $positional_2
16 #end if 22 #end if
17 23
18 > $default]]></command> 24 --outfile $default]]></command>
19 <inputs> 25 <inputs>
20 <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/> 26 <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/>
21 <param area="false" label="fastaq barcode library." name="positional_2" type="data" format="fastq"/> 27 <param area="false" label="fastaq barcode library." name="positional_2" type="data" format="fastq"/>
22 </inputs> 28 </inputs>
23 <outputs> 29 <outputs>