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comparison bamparse.xml @ 2:8ea06787c08a draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
author artbio
date Tue, 09 Oct 2018 17:14:57 -0400
parents ae9ea0488850
children 120eb76aa500
comparison
equal deleted inserted replaced
1:ae9ea0488850 2:8ea06787c08a
1 <tool id="bamparse" name="Count alignments" version="2.0.1"> 1 <tool id="bamparse" name="Count alignments" version="3.0.0">
2 <description>in a BAM file</description> 2 <description>in a BAM file</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.2">bowtie</requirement>
5 <requirement type="package" version="1.11.2">numpy</requirement>
6 <requirement type="package" version="0.11.2.1">pysam</requirement> 4 <requirement type="package" version="0.11.2.1">pysam</requirement>
5 <requirement type="package" version="0.6.6">sambamba</requirement>
7 </requirements> 6 </requirements>
8 <stdio> 7 <stdio>
9 <exit_code range="1:" level="fatal" description="Tool exception" /> 8 <exit_code range="1:" level="fatal" description="Tool exception" />
10 </stdio> 9 </stdio>
11 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
12 mkdir outputdir && 11 mkdir outputdir &&
12 #if $polarity == 'sense':
13 #set pol=' and not reverse_strand'
14 #else if $polarity == 'antisense':
15 #set pol=' and reverse_strand'
16 #else:
17 #set pol=''
18 #end if
13 #for $file in $input_list 19 #for $file in $input_list
14 samtools index '$file' && 20 sambamba view -t \$GALAXY_SLOTS -F "not unmapped$pol" -f bam '$file' -o '$file.element_identifier' &&
21 samtools index '$file.element_identifier' &&
15 #end for 22 #end for
16 python $__tool_directory__/bamparse.py 23 python $__tool_directory__/bamparse.py
17 --alignments 24 --alignments
18 #for $file in $input_list 25 #for $file in $input_list
19 '$file' 26 '$file.element_identifier'
20 #end for 27 #end for
21 --labels 28 --labels
22 #for $file in $input_list 29 #for $file in $input_list
23 '$file.element_identifier' 30 '$file.element_identifier'
24 #end for 31 #end for
25 --polarity '$polarity'
26 --number '$output_option' 32 --number '$output_option'
27 ]]></command> 33 ]]></command>
28 <inputs> 34 <inputs>
29 <param name="input_list" type="data" format="bam" label="Select multiple alignments to parse" multiple="true"/> 35 <param name="input_list" type="data" format="bam" label="Select multiple alignments to parse" multiple="true"/>
30 <param name="polarity" type="select" label="how to count sense and antisense reads"> 36 <param name="polarity" type="select" label="how to count sense and antisense reads">
42 <outputs> 48 <outputs>
43 <data name="output" format="tabular" label="Counts"> 49 <data name="output" format="tabular" label="Counts">
44 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.tabular" ext="tabular" visible="true" assign_primary_output="true" directory="outputdir"/> 50 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.tabular" ext="tabular" visible="true" assign_primary_output="true" directory="outputdir"/>
45 </data> 51 </data>
46 </outputs> 52 </outputs>
53 <tests>
54 <test>
55 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
56 <param name="polarity" value="both" />
57 <param name="output_option" value="unique" />
58 <output name="output" ftype="tabular" file="table.tabular" />
59 </test>
60 <test>
61 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
62 <param name="polarity" value="both" />
63 <param name="output_option" value="multiple" />
64 <output name="output" ftype="tabular" file="table0.tabular">
65 <discovered_dataset designation="table1" ftype="tabular" file="table1.tabular" />
66 </output>
67 </test>
68 <test>
69 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
70 <param name="polarity" value="sense" />
71 <param name="output_option" value="unique" />
72 <output name="output" ftype="tabular" file="table.tabular" />
73 </test>
74 <test>
75 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
76 <param name="polarity" value="antisense" />
77 <param name="output_option" value="unique" />
78 <output name="output" ftype="tabular" file="table_antisense.tabular" />
79 </test>
80
81 <test>
82 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
83 <param name="polarity" value="both" />
84 <param name="output_option" value="multiple" />
85 <output name="output" ftype="tabular" file="more_table0.tabular">
86 <discovered_dataset designation="table1" ftype="tabular" file="more_table1.tabular" />
87 <discovered_dataset designation="table2" ftype="tabular" file="more_table2.tabular" />
88 </output>
89 </test>
90 <test>
91 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
92 <param name="polarity" value="sense" />
93 <param name="output_option" value="unique" />
94 <output name="output" ftype="tabular" file="more_sense_table.tabular" />
95 </test>
96 <test>
97 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
98 <param name="polarity" value="antisense" />
99 <param name="output_option" value="unique" />
100 <output name="output" ftype="tabular" file="more_antisense_table.tabular" />
101 </test>
102
103
104 </tests>
47 <help> 105 <help>
48 106
49 **What it does** 107 **What it does**
50 108
51 Counts the number of reads aligned to each reference (@SN, reference NAME) in one or 109 Counts the number of reads aligned to each reference (@SN, reference NAME) in one or
54 Sense, antisense or both sense and antisense alignments can be counted 112 Sense, antisense or both sense and antisense alignments can be counted
55 113
56 The library labels in the returned count table are taken from the input bam datasets 114 The library labels in the returned count table are taken from the input bam datasets
57 names in the Galaxy history. 115 names in the Galaxy history.
58 </help> 116 </help>
59 <tests>
60 <test>
61 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="tabular" />
62 <param name="polarity" value="both" />
63 <param name="output_option" value="unique" />
64 <output name="output" ftype="tabular" file="table.tabular" />
65 </test>
66 <test>
67 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="tabular" />
68 <param name="polarity" value="both" />
69 <param name="output_option" value="multiple" />
70 <output name="output" ftype="tabular" file="table0.tabular">
71 <discovered_dataset designation="table1" ftype="tabular" file="table1.tabular" />
72 </output>
73 </test>
74 </tests>
75 </tool> 117 </tool>