Mercurial > repos > iuc > samtools_coverage

annotate samtools_coverage.xml @ 0:90f2dd176d80 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
author iuc
date Tue, 28 Sep 2021 15:10:16 +0000
parents
children ae36fab06bc2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
1 <tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@" profile="@PROFILE@">
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
2 <description>computes the depth at each position or region</description>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
3 <macros>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
5 </macros>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
7 <expand macro="stdio"/>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
8 <expand macro="version_command"/>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
9 <command><![CDATA[
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
10 @PREPARE_IDX@
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
11 samtools coverage
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
12
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
13 #if $condition_input.input_pooling == "Yes":
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
14 ${ ' '.join( [ "'%s'" % $x for $x in $condition_input.input] ) }
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
15 #else
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
16 '$condition_input.input'
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
17 #end if
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
18
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
19 -l $additional_options.min_read_length
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
20 -q $additional_options.min_mq
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
21 -Q $additional_options.min_bq
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
22
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
23 #set $filter = $additional_options.required_flags
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
24 @FLAGS@
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
25 -rf $flags
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
26
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
27 #set $filter = $additional_options.skipped_flags
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
28 @FLAGS@
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
29 -ff $flags
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
30
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
31 #if $condition_histogram.histogram_select == "yes"
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
32 -m
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
33 -w $condition_histogram.n_bins
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
34 #if $condition_histogram.region != "":
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
35 -r '$condition_histogram.region'
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
36 #end if
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
37 #end if
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
38
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
39 -o '$output'
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
40 ]]></command>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
41 <inputs>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
42 <conditional name="condition_input">
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
43 <param name="input_pooling" type="select" label="Are you pooling bam files?" help="Calculate the coverage for multiple bam files" >
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
44 <option value="No" selected="True">No</option>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
45 <option value="Yes">Yes</option>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
46 </param>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
47 <when value="No" >
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
48 <param name="input" type="data" format="bam" multiple="true" label="BAM file"/>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
49 </when>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
50 <when value="Yes">
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
51 <param name="input" type="data" format="bam" multiple="true" label="BAM files to be pooled"/>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
52 </when>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
53 </conditional>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
54
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
55 <section name="additional_options" title="Additional Options" expanded="true">
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
56 <param name="min_read_length" argument="-l" type="integer" min="0" value="0" label="Minimum read length" help="Ignore reads shorter than INT base pairs (Default = 0)" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
57 <param name="min_mq" argument="-q" type="integer" min="0" value="0" label="Minimum mapping quality" help="Minimum mapping quality for an alignment to be used (Default = 0)" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
58 <param name="min_bq" argument="-Q" type="integer" min="0" value="0" label="Minimum base quality" help="Minimum base quality for a base to be considered (Default = 0)" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
59
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
60 <param name="required_flags" argument="--rf" type="select" multiple="True" label="Require that these flags are set">
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
61 <expand macro="flag_options" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
62 </param>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
63
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
64 <param name="skipped_flags" argument="--ff" type="select" multiple="True" label="Exclude reads with any of the following flags set">
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
65 <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
66 </param>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
67 </section>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
68
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
69 <conditional name="condition_histogram">
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
70 <param name="histogram_select" argument="-m" type="select" label="Histogram" help="Show histogram instead of tabular output">
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
71 <option value="no" selected="true">No</option>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
72 <option value="yes">Yes</option>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
73 </param>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
74 <when value="yes">
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
75 <param name="n_bins" argument="-w" type="integer" min="1" value="100" label="Number of bins in histogram" help="Number of bins in histogram" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
76 <param name="region" argument="-r" type="text" value="" label="Show specified region" help="Show specified region. Format: chr:start-end." />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
77 </when>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
78 <when value="no" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
79 </conditional>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
80 </inputs>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
81
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
82 <outputs>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
83 <data name="output" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
84 </outputs>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
85
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
86 <tests>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
87 <test>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
88 <param name="input" value="test_1.bam" ftype="bam" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
89 <output name="output" file="results_1.tabular" ftype="tabular" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
90 </test>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
91 <test>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
92 <param name="input" value="test_1.bam" ftype="bam" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
93 <param name="histogram_select" value="yes" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
94 <param name="n_bins" value="50" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
95 <output name="output" file="results_2.txt" ftype="tabular" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
96 </test>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
97 <test>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
98 <param name="input_pooling" value="Yes" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
99 <param name="input" value="test_1.bam,test_2.bam" ftype="bam" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
100 <param name="histogram_select" value="yes" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
101 <param name="n_bins" value="100" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
102 <output name="output" file="results_3.txt" ftype="tabular" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
103 </test>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
104 </tests>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
105 <help><![CDATA[
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
106 **What it does**
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
107
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
108 This tool runs the ``samtools coverage`` command.
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
109
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
110 Computes the depth at each position or region and draws an ASCII-art histogram or tabulated text. If you select to pool the bam files, then it calculates coverage for the combined files.
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
111
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
112 The tabulated form uses the following headings:
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
113
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
114 - rname Reference name / chromosome
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
115 - startpos Start position
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
116 - endpos End position (or sequence length)
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
117 - numreads Number reads aligned to the region (after filtering)
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
118 - covbases Number of covered bases with depth >= 1
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
119 - coverage Proportion of covered bases [0..1]
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
120 - meandepth Mean depth of coverage
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
121 - meanbaseq Mean baseQ in covered region
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
122 - meanmapq Mean mapQ of selected reads
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
123
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
124 ]]></help>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
125 <expand macro="citations"/>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
diff changeset
126 </tool>