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comparison samtools_flagstat.xml @ 3:cc61ade70eb8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:18:29 -0400
parents 0072bf593791
children 4e404acfafa6
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2:0072bf593791 3:cc61ade70eb8
1 <tool id="samtools_flagstat" name="Flagstat" version="2.0"> 1 <tool id="samtools_flagstat" name="Flagstat" version="2.0.1">
2 <description>tabulate descriptive stats for BAM datset</description> 2 <description>tabulate descriptive stats for BAM datset</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
8 <expand macro="version_command"></expand>
9 <command>samtools flagstat "$input1" > "$output1"
10 </command>
11 <inputs>
12 <param name="input1" type="data" format="bam" label="BAM File to Convert" />
13 </inputs>
14 <outputs>
15 <data name="output1" format="txt" />
16 </outputs>
17 <tests>
18 <test>
19 <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
20 <output name="output1" file="samtools_flagstat_out1.txt" />
21 </test>
22 </tests>
23 <help>
24 3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <expand macro="version_command"/>
10
11 <command><![CDATA[
12 samtools flagstat '$input1' > '$output1'
13 ]]></command>
14
15 <inputs>
16 <param name="input1" type="data" format="bam" label="BAM File to report statistics of" />
17 </inputs>
18
19 <outputs>
20 <data name="output1" format="txt" />
21 </outputs>
22
23 <tests>
24 <test>
25 <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
26 <output name="output1" file="samtools_flagstat_out1.txt" />
27 </test>
28 </tests>
29 <help><![CDATA[
25 **What it does** 30 **What it does**
26 31
27 Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information:: 32 Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information::
28 33
29 200 + 0 in total (QC-passed reads + QC-failed reads) 34 200 + 0 in total (QC-passed reads + QC-failed reads)
30 0 + 0 secondary 35 0 + 0 secondary
31 0 + 0 supplementary 36 0 + 0 supplementary
32 0 + 0 duplicates 37 0 + 0 duplicates
33 25 + 0 mapped (12.50%:nan%) 38 25 + 0 mapped (12.50%:nan%)
34 200 + 0 paired in sequencing 39 200 + 0 paired in sequencing
37 0 + 0 properly paired (0.00%:nan%) 42 0 + 0 properly paired (0.00%:nan%)
38 0 + 0 with itself and mate mapped 43 0 + 0 with itself and mate mapped
39 25 + 0 singletons (12.50%:nan%) 44 25 + 0 singletons (12.50%:nan%)
40 0 + 0 with mate mapped to a different chr 45 0 + 0 with mate mapped to a different chr
41 0 + 0 with mate mapped to a different chr (mapQ>=5) 46 0 + 0 with mate mapped to a different chr (mapQ>=5)
42 47 ]]></help>
43 </help> 48 <expand macro="citations"/>
44 <expand macro="citations"></expand>
45 </tool> 49 </tool>