annotate bam2wig.xml @ 62:473382134e56 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author iuc
date Wed, 22 Feb 2023 15:06:01 +0000
parents 5968573462fa
children 27e16a30667a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
60
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
iuc
parents: 59
diff changeset
1 <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
2 <description>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
3 converts all types of RNA-seq data from .bam to .wig
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
4 </description>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
5 <macros>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
6 <import>rseqc_macros.xml</import>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
7 </macros>
61
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents: 60
diff changeset
8
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents: 60
diff changeset
9 <expand macro="bio_tools"/>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
10
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
11 <expand macro="requirements" />
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
12
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
13 <expand macro="stdio" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
14
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
15 <version_command><![CDATA[bam2wig.py --version]]></version_command>
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
16
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
17 <command><![CDATA[
60
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
iuc
parents: 59
diff changeset
18 @BAM_SAM_INPUTS@
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
iuc
parents: 59
diff changeset
19 bam2wig.py -i 'input.${extension}' -s '${chromsize}' -o outfile
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
20
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
21 #if str($strand_type.strand_specific) == "pair"
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
22 -d
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
23 #if str($strand_type.pair_type) == "sd"
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
24 '1++,1--,2+-,2-+'
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
25 #else
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
26 '1+-,1-+,2++,2--'
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
27 #end if
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
28 #end if
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
29
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
30 #if str($strand_type.strand_specific) == "single"
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
31 -d
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
32 #if str($strand_type.single_type) == "s"
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
33 '++,--'
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
34 #else
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
35 '+-,-+'
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
36 #end if
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
37 #end if
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
38
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
39 #if str($wigsum_type.wigsum_type_selector) == "normalize":
53
080fd5739bb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 734a31ae8ba22f0d75bda696c4856ee3e274e1ba
iuc
parents: 51
diff changeset
40 -t ${wigsum_type.totalwig}
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
41 #end if
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
42
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
43 @MULTIHITS@
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
44 ]]>
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
45 </command>
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
46 <inputs>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
47 <expand macro="bam_param" />
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
48 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
49 <expand macro="multihits_param" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
50 <conditional name="wigsum_type">
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
51 <param name="wigsum_type_selector" type="select" label="Normalization">
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
52 <option value="normalize">Normalize to specified sum</option>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
53 <option value="raw" selected="true">Do not normalize</option>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
54 </param>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
55 <when value="normalize">
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
56 <param name="totalwig" value="" type="integer" label="specified wigsum" help="(--wigsum)"/>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
57 </when>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
58 <when value="raw"/>
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
59 </conditional>
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
60 <expand macro="strand_type_param" />
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
61 </inputs>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
62
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
63 <outputs>
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
64 <data format="wig" name="output" from_work_dir="outfile.wig">
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
65 <filter>strand_type['strand_specific'] == 'none'</filter>
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
66 </data>
61
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents: 60
diff changeset
67 <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string}: forward reads">
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
68 <filter>strand_type['strand_specific'] != 'none'</filter>
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
69 </data>
61
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
parents: 60
diff changeset
70 <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string}: reverse reads">
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
71 <filter>strand_type['strand_specific'] != 'none'</filter>
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
72 </data>
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
73 </outputs>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
74
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
75 <tests>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
76 <test>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
77 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
78 <param name="chromsize" value="hg19.chrom.sizes"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
79 <output name="output" file="testwig.wig"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
80 </test>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
81 <test>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
82 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
83 <param name="chromsize" value="hg19.chrom.sizes"/>
53
080fd5739bb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 734a31ae8ba22f0d75bda696c4856ee3e274e1ba
iuc
parents: 51
diff changeset
84 <param name="multihits_type_selector" value="skip_multihits"/>
080fd5739bb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 734a31ae8ba22f0d75bda696c4856ee3e274e1ba
iuc
parents: 51
diff changeset
85 <param name="mapq" value="20"/>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
86 <output name="output" file="testwig.wig"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
87 </test>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
88 <test>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
89 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
90 <param name="chromsize" value="hg19.chrom.sizes"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
91 <param name="strand_specific" value="pair"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
92 <param name="pair_type" value="sd"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
93 <output name="outputfwd" file="testwig.Forward.wig"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
94 <output name="outputrv" file="testwig.Reverse.wig"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
95 </test>
53
080fd5739bb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 734a31ae8ba22f0d75bda696c4856ee3e274e1ba
iuc
parents: 51
diff changeset
96 <test>
080fd5739bb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 734a31ae8ba22f0d75bda696c4856ee3e274e1ba
iuc
parents: 51
diff changeset
97 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
080fd5739bb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 734a31ae8ba22f0d75bda696c4856ee3e274e1ba
iuc
parents: 51
diff changeset
98 <param name="chromsize" value="hg19.chrom.sizes"/>
080fd5739bb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 734a31ae8ba22f0d75bda696c4856ee3e274e1ba
iuc
parents: 51
diff changeset
99 <param name="wigsum_type_selector" value="normalize"/>
080fd5739bb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 734a31ae8ba22f0d75bda696c4856ee3e274e1ba
iuc
parents: 51
diff changeset
100 <param name="totalwig" value="100"/>
080fd5739bb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 734a31ae8ba22f0d75bda696c4856ee3e274e1ba
iuc
parents: 51
diff changeset
101 <output name="output" file="testwig_wigsum100.wig"/>
080fd5739bb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 734a31ae8ba22f0d75bda696c4856ee3e274e1ba
iuc
parents: 51
diff changeset
102 </test>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
103 </tests>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
104
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
105 <help><![CDATA[
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
106 bam2wig.py
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
107 ++++++++++
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
108
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
109 Visualization is the most straightforward and effective way to QC your RNA-seq
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
110 data. For example, change of expression or new splicing can be easily checked
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
111 by visually comparing two RNA-seq tracks using genome browser such as UCSC_,
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
112 IGB_ and IGV_. `bam2wig.py` converts all types of RNA-seq data from BAM_
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
113 format into wiggle_ format in one-stop. wiggle_ files can then be easily
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
114 converted into bigwig_. Bigwig is indexed, binary format of wiggle file, and
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
115 it's particular useful to display large, continuous dataset on genome
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
116 browser.
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
117
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
118 Inputs
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
119 ++++++++++++++
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
120
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
121 Input BAM file
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
122 Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools.
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
123
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
124 Chromosome size file
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
125 Tab or space separated text file with 2 columns: first column is chromosome name, second column is size of the chromosome. Chromosome names (such as "chr1") should be consistent between this file and BAM file.
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
126
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
127 Specified wigsum (default=none)
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
128 Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization.
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
129
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
130 Skip multiple Hit reads
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
131 skips multiple hit reads or only use uniquely mapped reads
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
132
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
133 Strand-specific (default=none)
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
134 How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
135
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
136 Outputs
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
137 ++++++++++++++
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
138
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
139 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
140 is strand specific, two wig files corresponding to Forward and Reverse will be generated.
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
141
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
142 @ABOUT@
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
143
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
144 .. _UCSC: http://genome.ucsc.edu/index.html
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
145 .. _IGB: http://bioviz.org/igb/
51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents: 49
diff changeset
146 .. _IGV: http://software.broadinstitute.org/software/igv/
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
147 .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
148 .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
149 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
150 ]]>
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
151 </help>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
152
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
153 <expand macro="citations" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 48
diff changeset
154
48
2e6190c29c54 Upload tar.gz again - toolshed removed all files (grrr...)
lparsons
parents:
diff changeset
155 </tool>