Mercurial > repos > devteam > bam_to_sam
comparison bam_to_sam.xml @ 4:3bade5114f21 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author | devteam |
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date | Tue, 13 Oct 2015 12:53:40 -0400 |
parents | 6eebf8420e31 |
children | eac9d3319326 |
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3:ad3c355b8249 | 4:3bade5114f21 |
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1 <tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.4"> | 1 <tool id="bam_to_sam" name="BAM-to-SAM" version="2.0"> |
2 <requirements> | 2 <macros> |
3 <requirement type="package" version="0.1.19">samtools</requirement> | 3 <import>macros.xml</import> |
4 </requirements> | 4 </macros> |
5 <description>converts BAM format to SAM format</description> | 5 <expand macro="requirements"></expand> |
6 <command interpreter="python"> | 6 <expand macro="version_command"></expand> |
7 bam_to_sam.py | 7 <expand macro="stdio"></expand> |
8 --input1=$input1 | 8 <description>convert BAM to SAM</description> |
9 --output1=$output1 | 9 <command> |
10 $header | 10 <![CDATA[ |
11 </command> | 11 samtools view -o "${output1}" ${header} "${input1}" |
12 <inputs> | 12 ]]> |
13 <param name="input1" type="data" format="bam" label="BAM File to Convert" /> | 13 </command> |
14 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" /> | 14 <inputs> |
15 </inputs> | 15 <param format="bam" label="BAM File to Convert" name="input1" type="data" /> |
16 <outputs> | 16 <param name="header" label="Header options" type="select" help="Allows to choose between seeing the entire dataset with the header, header only, or data only."> |
17 <data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" /> | 17 <option value="-h">Include header in SAM output (-h)</option> |
18 </outputs> | 18 <option value="-H">Print header only (-H)</option> |
19 <tests> | 19 <option value="">Exclude header</option> |
20 <test> | 20 </param> |
21 <!-- | 21 </inputs> |
22 Bam-to-Sam command: | 22 <outputs> |
23 samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam | 23 <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" /> |
24 bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam | 24 </outputs> |
25 --> | 25 <tests> |
26 <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" /> | 26 <test> |
27 <param name="header" value="" /> | 27 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> |
28 <output name="output1" file="bam_to_sam_out1.sam" sorted="True" /> | 28 <param name="header" value="-h" /> |
29 </test> | 29 <output file="bam_to_sam_out1.sam" name="output1" sorted="True" /> |
30 <test> | 30 </test> |
31 <!-- | 31 <test> |
32 Bam-to-Sam command: | 32 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> |
33 samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam | 33 <param name="header" value="-H" /> |
34 bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam | 34 <output file="bam_to_sam_out2.sam" name="output1" sorted="True" /> |
35 --> | 35 </test> |
36 <param name="input1" value="bam_to_sam_in2.bam" ftype="bam" /> | 36 <test> |
37 <param name="header" value="" /> | 37 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> |
38 <output name="output1" file="bam_to_sam_out2.sam" sorted="True" /> | 38 <param name="header" value="" /> |
39 </test> | 39 <output file="bam_to_sam_out3.sam" name="output1" sorted="True" /> |
40 <test> | 40 </test> |
41 <!-- | 41 </tests> |
42 Bam-to-Sam command: | 42 <help> |
43 samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam | 43 <![CDATA[ |
44 bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam | |
45 --> | |
46 <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" /> | |
47 <param name="header" value="--header" /> | |
48 <output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) --> | |
49 </test> | |
50 </tests> | |
51 <help> | |
52 | 44 |
53 **What it does** | 45 **What it does** |
54 | 46 |
55 This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. | 47 Converts BAM dataset to SAM using ``samtools view`` command:: |
56 | 48 |
57 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml | 49 samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM] |
58 | 50 |
51 ]]> | |
59 </help> | 52 </help> |
60 <citations> | 53 <expand macro="citations"></expand> |
61 <citation type="doi">10.1093/bioinformatics/btp352</citation> | |
62 </citations> | |
63 </tool> | 54 </tool> |