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comparison tools/mira4_0/mira4_mapping.xml @ 4:1713289d9908 draft default tip

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v0.0.11 tweak for use with bioconda dependencies
author peterjc
date Thu, 10 Aug 2017 11:09:10 -0400
parents a4f602cc3aa9
children
comparison
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3:a4f602cc3aa9 4:1713289d9908
1 <tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.9"> 1 <tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.11">
2 <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description> 2 <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">mira</requirement>
5 <requirement type="binary">miraconvert</requirement>
6 <requirement type="package" version="4.0.2">MIRA</requirement> 4 <requirement type="package" version="4.0.2">MIRA</requirement>
7 <requirement type="binary">samtools</requirement>
8 <requirement type="package" version="0.1.19">samtools</requirement> 5 <requirement type="package" version="0.1.19">samtools</requirement>
9 </requirements> 6 </requirements>
10 <stdio> 7 <version_command>
11 <!-- Assume anything other than zero is an error --> 8 python $__tool_directory__/mira4.py --version
12 <exit_code range="1:" /> 9 </version_command>
13 <exit_code range=":-1" /> 10 <command detect_errors="aggressive">
14 </stdio> 11 python $__tool_directory__/mira4.py
15 <version_command interpreter="python">mira4.py --version</version_command> 12 --manifest '$manifest'
16 <command interpreter="python">mira4.py
17 --manifest "$manifest"
18 #if str($maf_wanted) == "true": 13 #if str($maf_wanted) == "true":
19 --maf "$out_maf" 14 --maf '$out_maf'
20 #end if 15 #end if
21 #if str($bam_wanted) == "true": 16 #if str($bam_wanted) == "true":
22 --bam "$out_bam" 17 --bam '$out_bam'
23 #end if 18 #end if
24 --fasta "$out_fasta" 19 --fasta '$out_fasta'
25 --log "$out_log" 20 --log '$out_log'
26 </command> 21 </command>
27 <configfiles> 22 <configfiles>
28 <configfile name="manifest"> 23 <configfile name="manifest">
29 project = MIRA 24 project = MIRA
30 job = mapping,${job_type},${job_quality} 25 job = mapping,${job_type},${job_quality}
119 </param> 114 </param>
120 <!-- TODO? Allow technology type for references? --> 115 <!-- TODO? Allow technology type for references? -->
121 <!-- TODO? Allow strain settings for reference(s) and reads? --> 116 <!-- TODO? Allow strain settings for reference(s) and reads? -->
122 <!-- TODO? Use a repeat to allow for multi-strain references? --> 117 <!-- TODO? Use a repeat to allow for multi-strain references? -->
123 <!-- TODO? Add strain to the mapping read groups? --> 118 <!-- TODO? Add strain to the mapping read groups? -->
124 <param name="references" type="data" format="fasta,fastq,mira" multiple="true" required="true" label="Backbone reference file(s)" 119 <param name="references" type="data" format="fasta,fastq,mira" multiple="true" optional="false" label="Backbone reference file(s)"
125 help="Multiple files allowed, for example one FASTA file per chromosome or plasmid." /> 120 help="Multiple files allowed, for example one FASTA file per chromosome or plasmid." />
126 <param name="strain_setup" type="select" label="Strain configuration (reference vs reads)"> 121 <param name="strain_setup" type="select" label="Strain configuration (reference vs reads)">
127 <option value="default">Different strains - mapping reads onto a related reference ('StrainX' vs 'ReferenceStrain')</option> 122 <option value="default">Different strains - mapping reads onto a related reference ('StrainX' vs 'ReferenceStrain')</option>
128 <option value="same">Same strain - mapping reads from same reference (all 'StrainX')</option> 123 <option value="same">Same strain - mapping reads from same reference (all 'StrainX')</option>
129 </param> 124 </param>
156 <option value="stlouis">St. Louis scheme (see notes)</option> 151 <option value="stlouis">St. Louis scheme (see notes)</option>
157 </param> 152 </param>
158 </when> 153 </when>
159 <when value="none" /><!-- no further questions --> 154 <when value="none" /><!-- no further questions -->
160 </conditional> 155 </conditional>
161 <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)" 156 <param name="filenames" type="data" format="fastq,mira" multiple="true" optional="false" label="Read file(s)"
162 help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." /> 157 help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
163 </repeat> 158 </repeat>
164 <param name="maf_wanted" type="boolean" label="Output mapping in MIRA's own format?" checked="False" /> 159 <param name="maf_wanted" type="boolean" label="Output mapping in MIRA's own format?" checked="false" />
165 <param name="bam_wanted" type="boolean" label="Convert mapping into BAM format?" checked="True" /> 160 <param name="bam_wanted" type="boolean" label="Convert mapping into BAM format?" checked="true" />
166 </inputs> 161 </inputs>
167 <outputs> 162 <outputs>
168 <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" /> 163 <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" />
169 <data name="out_bam" format="bam" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly (BAM)"> 164 <data name="out_bam" format="bam" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly (BAM)">
170 <filter>bam_wanted is True</filter> 165 <filter>bam_wanted is True</filter>