Mercurial > repos > scottx611x > qualimap2_bamqc

annotate qualimap_bamqc.xml @ 3:c9afc13316ec draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
author scottx611x
date Wed, 25 Jul 2018 12:05:20 -0400
parents 5b36882f6455
children 5cdadbdf021f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
1 <?xml version="1.0" encoding="utf-8" ?>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
2 <tool id="qualimap_bamqc" name="QualiMap BamQC" version="2.2">
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
3 <description>Tool to to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.</description>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
4 <requirements>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
5 <requirement type="package" version="2.2">qualimap</requirement>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
6 </requirements>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
7 <stdio>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
8 <exit_code range=":-1" />
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
9 <exit_code range="1:" />
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
10 </stdio>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
11 <command interpreter="python">
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
12 qualimap_bamqc.py
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
13 --input_file $input_realigned_bam_file
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
14 --out_dir qualimap_results
3
c9afc13316ec planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
scottx611x
parents: 2
diff changeset
15 --out_genome_file $genome_coverage
0
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
16 --java_mem_size $mem_size
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
17 </command>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
18 <inputs>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
19 <param name="input_realigned_bam_file" type="data" format="bam" label="Realigned BAM dataset" help="Specify realigned BAM dataset"/>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
20 <param name="mem_size" type="text" value="8G" format="txt" label="Java memory size (default Gig)" help="Specify the size of memory to allocate. (Default 8 Gig)"/>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
21 </inputs>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
22 <outputs>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
23 <data format="txt" name="genome_results" label="Qualimap BamQC report">
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
24 <discover_datasets pattern="genome_results*" visible="true" ext="txt" directory="qualimap_results" assign_primary_output="true"/>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
25 </data>
2
5b36882f6455 planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents: 0
diff changeset
26 <data format="txt" name="genome_coverage" label="Qualimap BamQC coverage report"></data>
0
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
27 <data format="html" name="qualimap_html_results" label="Qualimap BamQC HTML report">
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
28 <discover_datasets pattern="qualimapReport*" visible="true" ext="html" directory="qualimap_results" assign_primary_output="true"/>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
29 </data>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
30 </outputs>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
31
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
32 <tests>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
33 <test>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
34 <param name="input_realigned_bam_file" value="test.bam"></param>
3
c9afc13316ec planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
scottx611x
parents: 2
diff changeset
35 <output name="genome_results">
c9afc13316ec planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
scottx611x
parents: 2
diff changeset
36 <assert_contents>
c9afc13316ec planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
scottx611x
parents: 2
diff changeset
37 <has_text text="" />
c9afc13316ec planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
scottx611x
parents: 2
diff changeset
38 </assert_contents>
0
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
39 </output>
3
c9afc13316ec planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
scottx611x
parents: 2
diff changeset
40 <output name="genome_coverage">
c9afc13316ec planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
scottx611x
parents: 2
diff changeset
41 <assert_contents>
c9afc13316ec planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
scottx611x
parents: 2
diff changeset
42 <has_text text="" />
c9afc13316ec planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
scottx611x
parents: 2
diff changeset
43 </assert_contents>
2
5b36882f6455 planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents: 0
diff changeset
44 </output>
3
c9afc13316ec planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
scottx611x
parents: 2
diff changeset
45 <output name="qualimap_html_results">
c9afc13316ec planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
scottx611x
parents: 2
diff changeset
46 <assert_contents>
c9afc13316ec planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
scottx611x
parents: 2
diff changeset
47 <has_text text="" />
c9afc13316ec planemo upload for repository https://github.com/scottx611x/qualimap2 commit 659800a1d841117a6fedc8ae394002c5744d1f2a
scottx611x
parents: 2
diff changeset
48 </assert_contents>
0
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
49 </output>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
50 </test>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
51 </tests>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
52 <help>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
53 https://github.com/scottx611x/qualimap2
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
54 </help>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
55 <citations>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
56 </citations>
d00bc4d82e90 Uploaded
scottx611x
parents:
diff changeset
57 </tool>