Mercurial > repos > wolma > mimodd

comparison bamsort.xml @ 5:bdd1995c9e66

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
upgrade to mimodd version 0.1.6.1
author Wolfgang Maier
date Tue, 28 Jul 2015 23:21:11 +0200
parents 72d20758ba2c
children 85214e4428fd
comparison
equal deleted inserted replaced
4:ffee8534a5c4 5:bdd1995c9e66
1 <tool id="bamsort" name="Sort BAM file"> 1 <tool id="bamsort" name="Sort BAM file" version="0.1.6.1">
2 <description>Sort a BAM file by coordinates (or names) of the mapped reads</description> 2 <description>Sort a BAM file by coordinates (or names) of the mapped reads</description>
3 <macros> 3 <macros>
4 <import>toolshed_macros.xml</import> 4 <import>toolshed_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>mimodd version -q</version_command> 7 <version_command>mimodd version -q</version_command>
8 <command> 8 <command>
9 mimodd sort "$inputfile" -o "$output" --oformat $oformat $by_name 9 mimodd sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name
10 </command> 10 </command>
11 11
12 <inputs> 12 <inputs>
13 <param name="inputfile" type="data" format="bam" label="Input file to sort" /> 13 <conditional name="input">
14 <param name="iformat" type="select" label = "Input data format">
15 <option value="bam">bam</option>
16 <option value="sam">sam</option>
17 </param>
18 <when value="bam">
19 <param name="ifile" type="data" format="bam" label="BAM input file to sort" />
20 </when>
21 <when value="sam">
22 <param name="ifile" type="data" format="sam" label="SAM input file to sort" />
23 </when>
24 </conditional>
25 <param name="oformat" type="select" label = "Output format for the sorted data">
26 <option value="bam">bam</option>
27 <option value="sam">sam</option>
28 </param>
14 <param name="by_name" type="boolean" truevalue = "-n" falsevalue ="" label="Sort by read names instead of coordinates" checked = "false" help="A less common option, but necessary, e.g., if you want to re-align sorted output from a previous run of the Snap Align Tool." /> 29 <param name="by_name" type="boolean" truevalue = "-n" falsevalue ="" label="Sort by read names instead of coordinates" checked = "false" help="A less common option, but necessary, e.g., if you want to re-align sorted output from a previous run of the Snap Align Tool." />
15 <param name="oformat" type="boolean" truevalue = "sam" falsevalue = "bam" label = "Output in uncompressed SAM format" checked = "false" />
16 </inputs> 30 </inputs>
17 31
18 <outputs> 32 <outputs>
19 <data name="output" format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}"> 33 <data name="output" format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}">
20 <change_format> 34 <change_format>