Mercurial > repos > devteam > bam_to_sam

annotate bam_to_sam.xml @ 4:3bade5114f21 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:53:40 -0400
parents 6eebf8420e31
children eac9d3319326
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
1 <tool id="bam_to_sam" name="BAM-to-SAM" version="2.0">
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
2 <macros>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
3 <import>macros.xml</import>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
4 </macros>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
5 <expand macro="requirements"></expand>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
6 <expand macro="version_command"></expand>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
7 <expand macro="stdio"></expand>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
8 <description>convert BAM to SAM</description>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
9 <command>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
10 <![CDATA[
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
11 samtools view -o "${output1}" ${header} "${input1}"
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
12 ]]>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
13 </command>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
14 <inputs>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
15 <param format="bam" label="BAM File to Convert" name="input1" type="data" />
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
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.">
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
17 <option value="-h">Include header in SAM output (-h)</option>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
18 <option value="-H">Print header only (-H)</option>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
19 <option value="">Exclude header</option>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
20 </param>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
21 </inputs>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
22 <outputs>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
23 <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" />
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
24 </outputs>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
25 <tests>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
26 <test>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
27 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
28 <param name="header" value="-h" />
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
29 <output file="bam_to_sam_out1.sam" name="output1" sorted="True" />
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
30 </test>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
31 <test>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
32 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
33 <param name="header" value="-H" />
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
34 <output file="bam_to_sam_out2.sam" name="output1" sorted="True" />
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
35 </test>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
36 <test>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
37 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
38 <param name="header" value="" />
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
39 <output file="bam_to_sam_out3.sam" name="output1" sorted="True" />
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
40 </test>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
41 </tests>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
42 <help>
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
43 <![CDATA[
0
c9e926d9d87e Uploaded tool tarball with dependencies.
devteam
parents:
diff changeset
44
c9e926d9d87e Uploaded tool tarball with dependencies.
devteam
parents:
diff changeset
45 **What it does**
c9e926d9d87e Uploaded tool tarball with dependencies.
devteam
parents:
diff changeset
46
4
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
47 Converts BAM dataset to SAM using ``samtools view`` command::
0
c9e926d9d87e Uploaded tool tarball with dependencies.
devteam
parents:
diff changeset
48
4
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
49 samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM]
0
c9e926d9d87e Uploaded tool tarball with dependencies.
devteam
parents:
diff changeset
50
4
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
51 ]]>
0
c9e926d9d87e Uploaded tool tarball with dependencies.
devteam
parents:
diff changeset
52 </help>
4
3bade5114f21 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 2
diff changeset
53 <expand macro="citations"></expand>
0
c9e926d9d87e Uploaded tool tarball with dependencies.
devteam
parents:
diff changeset
54 </tool>