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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
author yhoogstrate
date Thu, 13 Aug 2015 07:51:54 -0400
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="numpy" version="1.9">
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4 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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7 <package name="cython" version="0.20.1">
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8 <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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9 </package>
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11 <package name="crossmap" version="0.1.9">
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12 <install version="1.0">
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13 <actions>
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14 <action sha256sum="2ebcd4d1bdc51f53e2f9630f9d302bd3abcc58affed0f066f0a5c439e72ae7e2" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.1.9.tar.gz</action>
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16 <action type="setup_python_environment">
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17 <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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18 <package name="cython" version="0.20.1" />
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19 </repository>
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20 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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21 <package name="numpy" version="1.9" />
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22 </repository>
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23 </action>
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25 <!-- CrossMap doesn't pick up the correct Cython path.
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26 Therefore install it with a manual shell_command instead
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27 of <package></package> inside a pyton_env. -->
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28 <action type="shell_command">
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29 export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp;
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31 python setup.py install --root $INSTALL_DIR
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32 </action>
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34 <action type="set_environment">
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35 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/site-packages</environment_variable>
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36 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/dist-packages</environment_variable>
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37 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable>
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39 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable>
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40 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
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41 </action>
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42 </actions>
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43 </install>
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44 <readme>
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45 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
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46 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
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47 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
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48 and VCF, reading from remote servers and file compression are supported.
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49
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50 NEWS:
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51 * 07/27/15: Release version 0.1.9. For VCF file conversion in v0.1.9:
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52 - CrossMap uses the indexed reference genome (target assembly) sequences rather than load
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53 the entire file into memory. Users could index their reference genome file using samtools faidx
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54 before running CrossMap, otherwise CrossMap will index it automatically the first time you run it.
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55 - In the output VCF file, whether the chromosome IDs contain "chr" or not depends on the input
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56 format.
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57 * 05/15/15: Release version 0.1.8: Fixed the bug that CrossMap will output invalid VCF file when the
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58 input VCF file contains a INFO field with whitespace.
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59 * 05/04/15: Release version 0.1.7: Address the problem that CrossMap does not convert strand in
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60 inversions when input file is BED6 or BED12 format.
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61 * 11/06/14: Release version 0.1.6: Fixed "negative coordinates" bug.
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62 * 08/05/14: Release version 0.1.5: Support compressed (*.gz, *.Z, *.z, *.bz, *.bz2, *.bzip2) wiggle file
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63 as input.
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64 * 05/19/14: add chain files for hg38-&gt;hg19, hg19-&gt;hg38, hg18-&gt;hg38, hg19-&gt;GRCh37,
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65 GRCh37-&gt;hg19. In CrossMap v0.1.4, conversion results of BAM/SAM files can be directed to
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66 STDOUT to support piping.
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67 * 12/12/13: CrossMap was accepted by Bioinformatics
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68 * 10/23/13: CrossMap (0.1.3) was released
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69
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70 Documentation: http://crossmap.sourceforge.net/
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71 </readme>
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72 </package>
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73 </tool_dependency>