Mercurial > repos > yhoogstrate > package_crossmap_0_2

annotate tool_dependencies.xml @ 2:e4de7f1284ce draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
author yhoogstrate
date Wed, 04 Nov 2015 10:11:28 -0500
parents 803db5577b07
children bbc4d67d6a37
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
1 <?xml version="1.0"?>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
2 <tool_dependency>
1
803db5577b07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
yhoogstrate
parents: 0
diff changeset
3 <package name="nose" version="1.3.7">
803db5577b07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
yhoogstrate
parents: 0
diff changeset
4 <repository changeset_revision="e0d81eee3c51" name="package_nose_1_3_7" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
803db5577b07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
yhoogstrate
parents: 0
diff changeset
5 </package>
803db5577b07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
yhoogstrate
parents: 0
diff changeset
6
0
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
7 <package name="numpy" version="1.9">
2
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
8 <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
0
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
9 </package>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
10
1
803db5577b07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
yhoogstrate
parents: 0
diff changeset
11 <package name="cython" version="0.23.1">
803db5577b07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
yhoogstrate
parents: 0
diff changeset
12 <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
0
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
13 </package>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
14
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
15 <package name="crossmap" version="0.2">
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
16 <install version="1.0">
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
17 <actions>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
18 <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
19
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
20 <action type="setup_python_environment">
1
803db5577b07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
yhoogstrate
parents: 0
diff changeset
21 <repository changeset_revision="e0d81eee3c51" name="package_nose_1_3_7" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu">
803db5577b07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
yhoogstrate
parents: 0
diff changeset
22 <package name="nose" version="1.3.7" />
803db5577b07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
yhoogstrate
parents: 0
diff changeset
23 </repository>
803db5577b07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
yhoogstrate
parents: 0
diff changeset
24 <repository changeset_revision="45abfe2b0cfc" name="package_cython_0_23_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
803db5577b07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095
yhoogstrate
parents: 0
diff changeset
25 <package name="cython" version="0.23.1" />
0
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
26 </repository>
2
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
27 <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
0
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
28 <package name="numpy" version="1.9" />
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
29 </repository>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
30 </action>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
31
2
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
32 <!-- If CrossMap is installed with - - home or - - prefix
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
33 into, it often crashes with a 'write-test' error
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
34
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
35 Using - - root places the installation in:
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
36 $INSTALL_DIR / (python path dir) /
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
37 -->
0
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
38 <action type="shell_command">
2
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
39 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ;
0
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
40
2
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
41 python setup.py install --root $INSTALL_DIR &amp;&amp;
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
42 export SUB_DIR=$(dirname $(which python)) &amp;&amp;
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
43 mv $INSTALL_DIR$SUB_DIR/../lib $INSTALL_DIR/lib &amp;&amp;
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
44 mv $INSTALL_DIR$SUB_DIR $INSTALL_DIR/bin
0
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
45 </action>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
46
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
47 <action type="set_environment">
2
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
48 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR"/lib/python2.7/site-packages"</environment_variable>
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
49 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
0
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
50
2
e4de7f1284ce planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7
yhoogstrate
parents: 1
diff changeset
51 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable>
0
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
52 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
53 </action>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
54 </actions>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
55 </install>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
56 <readme>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
57 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
58 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
59 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
60 and VCF, reading from remote servers and file compression are supported.
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
61
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
62 NEWS:
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
63 * 08/11/15: Release version 0.2: Fixed the bug that CrossMap will not convert wiggle format files due to name collision with bx python.
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
64 * 07/27/15: Release version 0.1.9. For VCF file conversion in v0.1.9:
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
65 - CrossMap uses the indexed reference genome (target assembly) sequences rather than load
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
66 the entire file into memory. Users could index their reference genome file using samtools faidx
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
67 before running CrossMap, otherwise CrossMap will index it automatically the first time you run it.
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
68 - In the output VCF file, whether the chromosome IDs contain "chr" or not depends on the input
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
69 format.
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
70 * 05/15/15: Release version 0.1.8: Fixed the bug that CrossMap will output invalid VCF file when the
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
71 input VCF file contains a INFO field with whitespace.
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
72 * 05/04/15: Release version 0.1.7: Address the problem that CrossMap does not convert strand in
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
73 inversions when input file is BED6 or BED12 format.
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
74 * 11/06/14: Release version 0.1.6: Fixed "negative coordinates" bug.
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
75 * 08/05/14: Release version 0.1.5: Support compressed (*.gz, *.Z, *.z, *.bz, *.bz2, *.bzip2) wiggle file
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
76 as input.
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
77 * 05/19/14: add chain files for hg38-&gt;hg19, hg19-&gt;hg38, hg18-&gt;hg38, hg19-&gt;GRCh37,
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
78 GRCh37-&gt;hg19. In CrossMap v0.1.4, conversion results of BAM/SAM files can be directed to
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
79 STDOUT to support piping.
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
80 * 12/12/13: CrossMap was accepted by Bioinformatics
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
81 * 10/23/13: CrossMap (0.1.3) was released
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
82
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
83 Documentation: http://crossmap.sourceforge.net/
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
84 </readme>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
85 </package>
805c8fbd3b4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
86 </tool_dependency>