Mercurial > repos > rnateam > mirdeep2_mapper

comparison mapper.xml @ 3:a8d24f4b6d95 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
author rnateam
date Wed, 12 Jul 2017 14:38:46 -0400
parents ab8cd78709e1
children dbbe92348c7a
comparison
equal deleted inserted replaced
2:ab8cd78709e1 3:a8d24f4b6d95
1 <tool id="rbc_mirdeep2_mapper" name="MiRDeep2 Mapper" version="2.0.0"> 1 <tool id="rbc_mirdeep2_mapper" name="MiRDeep2 Mapper" version="2.0.0">
2 <description>process and map reads to a reference genome</description>
2 <macros> 3 <macros>
3 <macro name="map_params"> 4 <macro name="map_params">
4 <conditional name="refGenomeSource"> 5 <conditional name="refGenomeSource">
5 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Map to genome. (-p)"> 6 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Map to genome. (-p)">
6 <option value="indexed">Use a built-in index</option> 7 <option value="indexed">Use a built-in index</option>
13 <validator type="no_options" message="No indexes are available for the selected input dataset"/> 14 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
14 </options> 15 </options>
15 </param> 16 </param>
16 </when> <!-- build-in --> 17 </when> <!-- build-in -->
17 <when value="history"> 18 <when value="history">
18 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> 19 <param name="ownFile" type="data" format="fasta" label="Select the reference genome" />
19 </when> <!-- history --> 20 </when> <!-- history -->
20 </conditional> <!-- refGenomeSource --> 21 </conditional> <!-- refGenomeSource -->
21 <param name="map_mismatch" type="boolean" truevalue="-q" falsevalue="" checked="false" label="Map with one mismatch in the seed (mapping takes longer)" help="(-q)"/> 22 <param name="map_mismatch" type="boolean" truevalue="-q" falsevalue="" checked="false" label="Map with one mismatch in the seed (mapping takes longer)" help="(-q)"/>
22 <param name="map_threshold" value="5" type="integer" optional="false" label="A read is allowed to map up to this number of positions in the genome" help="Map threshold. (-r)"> 23 <param name="map_threshold" value="5" type="integer" optional="false" label="A read is allowed to map up to this number of positions in the genome" help="Map threshold. (-r)">
23 <validator type="in_range" min="1" message="Minimum value is 1"/> 24 <validator type="in_range" min="1" message="Minimum value is 1"/>
24 </param> 25 </param>
25 </macro> 26 </macro>
26 </macros> 27 </macros>
27 <description>
28 <![CDATA[
29 process and map reads to a reference genome
30 ]]>
31 </description>
32 <requirements> 28 <requirements>
33 <requirement type="package" version="2.0">mirdeep2_mapper</requirement> 29 <requirement type="package" version="2.0.0.8">mirdeep2</requirement>
34 <requirement type="package" version="0.12.7">bowtie</requirement>
35 <requirement type="package" version="5.18.1">perl</requirement>
36 </requirements> 30 </requirements>
37 31 <stdio>
32 <!-- Anything other than zero is an error -->
33 <exit_code range="1:" />
34 <exit_code range=":-1" />
35 <!-- In case the return code has not been set propery check stderr too -->
36 <regex match="Error:" />
37 <regex match="Exception:" />
38 </stdio>
38 <command> 39 <command>
39 <![CDATA[ 40 <![CDATA[
40 41
41 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map" 42 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map"
42 #if $operation.refGenomeSource.genomeSource == "history" 43 #if $operation.refGenomeSource.genomeSource == "history"
84 #end if 85 #end if
85 86
86 -v -n 87 -v -n
87 ]]> 88 ]]>
88 </command> 89 </command>
89 <stdio>
90 <!-- Anything other than zero is an error -->
91 <exit_code range="1:" />
92 <exit_code range=":-1" />
93 <!-- In case the return code has not been set propery check stderr too -->
94 <regex match="Error:" />
95 <regex match="Exception:" />
96 </stdio>
97 <inputs> 90 <inputs>
98 <param format="fastq, fasta" name="reads" type="data" optional="false" label="Deep sequencing reads" help="Reads in fastq or FASTA format"/> 91 <param format="fastq, fasta" name="reads" type="data" optional="false" label="Deep sequencing reads" help="Reads in fastq or FASTA format"/>
99 <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)"/> 92 <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)"/>
100 <param name="convert_rna_dna" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Convert RNA to DNA alphabet (to map against genome)" help="(-i)"/> 93 <param name="convert_rna_dna" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Convert RNA to DNA alphabet (to map against genome)" help="(-i)"/>
101 94