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comparison samtools_flagstat.xml @ 7:fe34990e5ce7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:13:41 +0000
parents 22970df7a40e
children fefd89ab563c
comparison
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6:22970df7a40e 7:fe34990e5ce7
1 <tool id="samtools_flagstat" name="Samtools flagstat" version="2.0.3"> 1 <tool id="samtools_flagstat" name="Samtools flagstat" version="2.0.4" profile="@PROFILE@">
2 <description>tabulate descriptive stats for BAM datset</description> 2 <description>tabulate descriptive stats for BAM datset</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <expand macro="version_command"/> 9 <expand macro="version_command"/>
10 10
11 <command><![CDATA[ 11 <command><![CDATA[
12 @ADDTHREADS@ 12 @ADDTHREADS@
13 samtools flagstat -@ \$addthreads '$input1' > '$output1' 13 samtools flagstat -@ \$addthreads
14 #if $output_fmt != 'txt'
15 --output-fmt $output_fmt
16 #end if
17 '$input1'
18 > '$output1'
14 ]]></command> 19 ]]></command>
15 20
16 <inputs> 21 <inputs>
17 <param name="input1" type="data" format="sam,bam,cram" label="BAM File to report statistics of" /> 22 <param name="input1" type="data" format="sam,bam,cram" label="BAM File to report statistics of" />
23 <param argument="--output-fmt" type="select" label="Output format">
24 <option value="txt">txt</option>
25 <option value="tsv">tsv</option>
26 <option value="json">json</option>
27 </param>
18 </inputs> 28 </inputs>
19 29
20 <outputs> 30 <outputs>
21 <data name="output1" format="txt" /> 31 <data name="output1" format="txt">
32 <change_format>
33 <when input="output_fmt" value="tsv" format="tabular" />
34 <when input="output_fmt" value="json" format="json" />
35 </change_format>
36 </data>
22 </outputs> 37 </outputs>
23 38
24 <tests> 39 <tests>
25 <test> 40 <test>
26 <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" /> 41 <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
27 <output name="output1" file="samtools_flagstat_out1.txt" /> 42 <output name="output1" file="samtools_flagstat_out1.txt" ftype="txt"/>
43 </test>
44 <test>
45 <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
46 <param name="output_fmt" value="tsv"/>
47 <output name="output1" file="samtools_flagstat_out1.tsv" ftype="tabular" />
48 </test>
49 <test>
50 <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
51 <param name="output_fmt" value="json"/>
52 <output name="output1" file="samtools_flagstat_out1.json" ftype="json" />
28 </test> 53 </test>
29 </tests> 54 </tests>
30 <help><![CDATA[ 55 <help><![CDATA[
31 **What it does** 56 **What it does**
32 57