Mercurial > repos > devteam > samtools_idxstats

comparison samtools_idxstats.xml @ 1:88b8c2916784 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_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:19:02 -0400
parents 87398ae795c7
children 04d5581db1f5
comparison
equal deleted inserted replaced
0:87398ae795c7 1:88b8c2916784
1 <tool id="samtools_idxstats" name="IdxStats" version="2.0"> 1 <tool id="samtools_idxstats" name="IdxStats" version="2.0.1">
2 <description>tabulate mapping statistics for BAM dataset</description> 2 <description>reports stats of the BAM index file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"/>
7 <expand macro="stdio"></expand> 7 <expand macro="stdio"/>
8 <expand macro="version_command"></expand> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 if [ ! -f "${input}.bai" ] ; then 10 ln -f -s '${input.metadata.bam_index}' '${input}.bai' &&
11 ln -s "${input}" input.bam ; 11
12 samtools sort -o sorted.bam -O bam -T sts "${input}" ; 12 samtools idxstats '${input}' > '${output}'
13 samtools index sorted.bam ; 13 ]]></command>
14 samtools idxstats sorted.bam > "${output}" ;
15 else
16 samtools idxstats "${input}" > "${output}" ;
17 fi]]>
18 </command>
19 <inputs> 14 <inputs>
20 <param name="input" type="data" format="bam" label="BAM file" /> 15 <param name="input" type="data" format="bam" label="BAM file" />
21 </inputs> 16 </inputs>
22 <outputs> 17 <outputs>
23 <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> 18 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
26 <test> 21 <test>
27 <param name="input" value="phiX.bam" ftype="bam" /> 22 <param name="input" value="phiX.bam" ftype="bam" />
28 <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" /> 23 <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" />
29 </test> 24 </test>
30 </tests> 25 </tests>
31 <help> 26 <help><![CDATA[
32 <![CDATA[
33 **What it does** 27 **What it does**
34 28
35 Runs the ``samtools idxstats`` command. It retrieves and prints stats in the index file. 29 Runs the ``samtools idxstats`` command. It retrieves and prints stats in the index file.
36 30
37 Input is a sorted and indexed BAM file, the output is tabular with 31 Input is a sorted and indexed BAM file, the output is tabular with
56 ... ... ... ... 50 ... ... ... ...
57 contig_603 653 50 0 51 contig_603 653 50 0
58 contig_604 214 6 0 52 contig_604 214 6 0
59 \* 0 0 50320 53 \* 0 0 50320
60 54
61
62 In this example there were 604 contigs, each with one line in the output table, 55 In this example there were 604 contigs, each with one line in the output table,
63 plus the final row (labelled with an asterisk) representing 50320 unmapped reads. 56 plus the final row (labelled with an asterisk) representing 50320 unmapped reads.
64 In this BAM file, the final column was otherwise zero. 57 In this BAM file, the final column was otherwise zero.
65 58
66 ------ 59 ------
67 60
68 Peter J.A. Cock (2013), `Galaxy wrapper <https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats>`_ for the samtools idxstats command 61 Peter J.A. Cock (2013), `Galaxy wrapper <https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats>`_ for the samtools idxstats command
69 ]]> 62 ]]></help>
70 </help> 63 <expand macro="citations"/>
71 <expand macro="citations"></expand>
72 </tool> 64 </tool>