Mercurial > repos > artbio > bamparse

annotate bamparse.xml @ 3:120eb76aa500 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
author artbio
date Mon, 17 Jul 2023 01:02:17 +0000
parents 8ea06787c08a
children 1997af8f4648
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
120eb76aa500 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
artbio
parents: 2
diff changeset
1 <tool id="bamparse" name="Count alignments" version="4.0.0">
0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
2 <description>in a BAM file</description>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
3 <requirements>
3
120eb76aa500 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
artbio
parents: 2
diff changeset
4 <requirement type="package" version="0.21.0=py310h41dec4a_1">pysam</requirement>
120eb76aa500 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
artbio
parents: 2
diff changeset
5 <requirement type="package" version="1.0=h98b6b92_0">sambamba</requirement>
120eb76aa500 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
artbio
parents: 2
diff changeset
6 <requirement type="package" version="1.17=hd87286a_1">samtools</requirement>
0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
7 </requirements>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
8 <stdio>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
9 <exit_code range="1:" level="fatal" description="Tool exception" />
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
10 </stdio>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
12 mkdir outputdir &&
2
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
13 #if $polarity == 'sense':
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
14 #set pol=' and not reverse_strand'
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
15 #else if $polarity == 'antisense':
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
16 #set pol=' and reverse_strand'
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
17 #else:
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
18 #set pol=''
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
19 #end if
0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
20 #for $file in $input_list
2
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
21 sambamba view -t \$GALAXY_SLOTS -F "not unmapped$pol" -f bam '$file' -o '$file.element_identifier' &&
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
22 samtools index '$file.element_identifier' &&
0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
23 #end for
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
24 python $__tool_directory__/bamparse.py
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
25 --alignments
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
26 #for $file in $input_list
2
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
27 '$file.element_identifier'
0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
28 #end for
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
29 --labels
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
30 #for $file in $input_list
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
31 '$file.element_identifier'
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
32 #end for
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
33 --number '$output_option'
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
34 ]]></command>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
35 <inputs>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
36 <param name="input_list" type="data" format="bam" label="Select multiple alignments to parse" multiple="true"/>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
37 <param name="polarity" type="select" label="how to count sense and antisense reads">
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
38 <option value="both">count both sense and antisense reads</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
39 <option value="sense">count only sense reads</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
40 <option value="antisense">count only antisense reads</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
41 </param>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
42 <param name="output_option" type="select" display="radio" label="Select the number of files for results"
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
43 help="Results can be returned either as a single multi-column table or in separate two-column
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
44 datasets (useful for DESeq subsequent analysis)">
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
45 <option value="unique">A multi-column table</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
46 <option value="multiple">One separate two-columns dataset per input bam alignment</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
47 </param>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
48 </inputs>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
49 <outputs>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
50 <data name="output" format="tabular" label="Counts">
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
51 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.tabular" ext="tabular" visible="true" assign_primary_output="true" directory="outputdir"/>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
52 </data>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
53 </outputs>
2
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
54 <tests>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
55 <test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
56 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
57 <param name="polarity" value="both" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
58 <param name="output_option" value="unique" />
3
120eb76aa500 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
artbio
parents: 2
diff changeset
59 <output name="output" ftype="tabular" file="table.tabular" count="1"/>
2
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
60 </test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
61 <test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
62 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
63 <param name="polarity" value="both" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
64 <param name="output_option" value="multiple" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
65 <output name="output" ftype="tabular" file="table0.tabular">
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
66 <discovered_dataset designation="table1" ftype="tabular" file="table1.tabular" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
67 </output>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
68 </test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
69 <test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
70 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
71 <param name="polarity" value="sense" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
72 <param name="output_option" value="unique" />
3
120eb76aa500 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
artbio
parents: 2
diff changeset
73 <output name="output" ftype="tabular" file="table.tabular" count="1"/>
2
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
74 </test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
75 <test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
76 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
77 <param name="polarity" value="antisense" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
78 <param name="output_option" value="unique" />
3
120eb76aa500 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
artbio
parents: 2
diff changeset
79 <output name="output" ftype="tabular" file="table_antisense.tabular" count="1"/>
2
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
80 </test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
81
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
82 <test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
83 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
84 <param name="polarity" value="both" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
85 <param name="output_option" value="multiple" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
86 <output name="output" ftype="tabular" file="more_table0.tabular">
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
87 <discovered_dataset designation="table1" ftype="tabular" file="more_table1.tabular" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
88 <discovered_dataset designation="table2" ftype="tabular" file="more_table2.tabular" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
89 </output>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
90 </test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
91 <test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
92 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
93 <param name="polarity" value="sense" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
94 <param name="output_option" value="unique" />
3
120eb76aa500 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
artbio
parents: 2
diff changeset
95 <output name="output" ftype="tabular" file="more_sense_table.tabular" count="1"/>
2
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
96 </test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
97 <test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
98 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
99 <param name="polarity" value="antisense" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
100 <param name="output_option" value="unique" />
3
120eb76aa500 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
artbio
parents: 2
diff changeset
101 <output name="output" ftype="tabular" file="more_antisense_table.tabular" count="1"/>
2
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
102 </test>
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
103
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
104
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
artbio
parents: 1
diff changeset
105 </tests>
0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
106 <help>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
107
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
108 **What it does**
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
109
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
110 Counts the number of reads aligned to each reference (@SN, reference NAME) in one or
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
111 several BAM alignments.
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
112
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
113 Sense, antisense or both sense and antisense alignments can be counted
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
114
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
115 The library labels in the returned count table are taken from the input bam datasets
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
116 names in the Galaxy history.
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
117 </help>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff changeset
118 </tool>