| Previous changeset 2:ab8cd78709e1 (2016-11-23) Next changeset 4:dbbe92348c7a (2018-04-05) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa |
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modified:
mapper.xml |
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removed:
tool_dependencies.xml |
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| diff -r ab8cd78709e1 -r a8d24f4b6d95 mapper.xml --- a/mapper.xml Wed Nov 23 16:32:13 2016 -0500 +++ b/mapper.xml Wed Jul 12 14:38:46 2017 -0400 |
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| @@ -1,4 +1,5 @@ <tool id="rbc_mirdeep2_mapper" name="MiRDeep2 Mapper" version="2.0.0"> + <description>process and map reads to a reference genome</description> <macros> <macro name="map_params"> <conditional name="refGenomeSource"> @@ -15,7 +16,7 @@ </param> </when> <!-- build-in --> <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> + <param name="ownFile" type="data" format="fasta" label="Select the reference genome" /> </when> <!-- history --> </conditional> <!-- refGenomeSource --> <param name="map_mismatch" type="boolean" truevalue="-q" falsevalue="" checked="false" label="Map with one mismatch in the seed (mapping takes longer)" help="(-q)"/> @@ -24,17 +25,17 @@ </param> </macro> </macros> - <description> -<![CDATA[ -process and map reads to a reference genome -]]> - </description> <requirements> - <requirement type="package" version="2.0">mirdeep2_mapper</requirement> - <requirement type="package" version="0.12.7">bowtie</requirement> - <requirement type="package" version="5.18.1">perl</requirement> + <requirement type="package" version="2.0.0.8">mirdeep2</requirement> </requirements> - + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> <command> <![CDATA[ @@ -86,14 +87,6 @@ -v -n ]]> </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> <inputs> <param format="fastq, fasta" name="reads" type="data" optional="false" label="Deep sequencing reads" help="Reads in fastq or FASTA format"/> <param name="remove_non_canon" type="boolean" truevalue="-j" falsevalue="" checked="false" label="Remove reads with non-standard nucleotides" help="Remove all entries that have a sequence that contains letters other than a,c,g,t,u,n,A,C,G,T,U,N. (-j)"/> |
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| diff -r ab8cd78709e1 -r a8d24f4b6d95 tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 23 16:32:13 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,65 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="perl" version="5.18.1"> - <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bowtie" version="0.12.7"> - <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="mirdeep2_mapper" version="2.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-mapper.tar.gz</action> - <action type="move_file"> - <source>clip_adapters.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>collapse_reads_md.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>convert_bowtie_output.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>fastaparse.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>fastq2fasta.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>illumina_to_fasta.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>mapper.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>parse_mappings.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>rna2dna.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme> - -Processes reads and/or maps them to the reference genome. - -input: -Default input is a file in fasta, seq.txt or qseq.txt format. More input can be given depending on the options used. -output: -The output depends on the options used (see below). Either a fasta file with processed reads or an arf file with with mapped reads, or both, are output. - - </readme> - </package> -</tool_dependency> |