Mercurial > repos > devteam > samtools_mpileup

comparison macros.xml @ 7:edbe9587b15d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 831f76c1ac20172b902d9edf79aced718feb96e2
author iuc
date Mon, 03 Sep 2018 13:09:45 -0400
parents 483949f5c3b0
children 6fc185405512
comparison
equal deleted inserted replaced
6:483949f5c3b0 7:edbe9587b15d
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3.1">samtools</requirement> 4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
5 <yield/> 5 <yield/>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8 <token name="@TOOL_VERSION@">1.3.1</token> 8 <token name="@TOOL_VERSION@">1.9</token>
9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
10 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
11 ##prepare input and indices
12 #for $i, $bam in enumerate( $input_bams ):
13 ln -s '$bam' '${i}' &&
14 #if $bam.is_of_type('bam'):
15 #if str( $bam.metadata.bam_index ) != "None":
16 ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
17 #else:
18 samtools index '${i}' '${i}.bai' &&
19 #end if
20 #elif $bam.is_of_type('cram'):
21 #if str( $bam.metadata.cram_index ) != "None":
22 ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
23 #else:
24 samtools index '${i}' '${i}.crai' &&
25 #end if
26 #end if
27 #end for
28 ]]></token>
29 <xml name="flag_options">
30 <option value="1">read is paired</option>
31 <option value="2">read is mapped in a proper pair</option>
32 <option value="4">read is unmapped</option>
33 <option value="8">mate is unmapped</option>
34 <option value="16">read reverse strand</option>
35 <option value="32">mate reverse strand</option>
36 <option value="64">read is the first in a pair</option>
37 <option value="128">read is the second in a pair</option>
38 <option value="256">alignment or read is not primary</option>
39 <option value="512">read fails platform/vendor quality checks</option>
40 <option value="1024">read is a PCR or optical duplicate</option>
41 <option value="2048">supplementary alignment</option>
42 </xml>
9 <xml name="citations"> 43 <xml name="citations">
10 <citations> 44 <citations>
11 <citation type="bibtex"> 45 <citation type="bibtex">
12 @misc{SAM_def, 46 @misc{SAM_def,
13 title={Definition of SAM/BAM format}, 47 title={Definition of SAM/BAM format},