Mercurial > repos > peterjc > mira4_assembler
comparison tools/mira4/mira4_mapping.xml @ 20:aeb3e35f8236 draft
Uploaded v0.0.4 preview, made MAF and BAM output optional
| author | peterjc |
|---|---|
| date | Tue, 10 Jun 2014 10:11:58 -0400 |
| parents | 8487d70e82aa |
| children | 4abe8d59a438 |
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| 19:8487d70e82aa | 20:aeb3e35f8236 |
|---|---|
| 1 <tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.3"> | 1 <tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.4"> |
| 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> | 4 <requirement type="binary">mira</requirement> |
| 5 <requirement type="binary">miraconvert</requirement> | 5 <requirement type="binary">miraconvert</requirement> |
| 6 <requirement type="package" version="4.0">MIRA</requirement> | 6 <requirement type="package" version="4.0">MIRA</requirement> |
| 7 <requirement type="binary">samtools</requirement> | 7 <requirement type="binary">samtools</requirement> |
| 8 <requirement type="package" version="0.1.19">samtools</requirement> | 8 <requirement type="package" version="0.1.19">samtools</requirement> |
| 9 </requirements> | 9 </requirements> |
| 10 <version_command interpreter="python">mira4.py --version</version_command> | 10 <version_command interpreter="python">mira4.py --version</version_command> |
| 11 <command interpreter="python"> | 11 <command interpreter="python">mira4.py |
| 12 mira4.py "$manifest" "$out_maf" "$out_bam" "$out_fasta" "$out_log" | 12 --manifest "$manifest" |
| 13 #if str($maf_wanted) == "true": | |
| 14 --maf "$out_maf" | |
| 15 #end if | |
| 16 #if str($bam_wanted) == "true": | |
| 17 --bam "$out_bam" | |
| 18 #end if | |
| 19 --fasta "$out_fasta" | |
| 20 --log "$out_log" | |
| 13 </command> | 21 </command> |
| 14 <stdio> | 22 <stdio> |
| 15 <!-- Assume anything other than zero is an error --> | 23 <!-- Assume anything other than zero is an error --> |
| 16 <exit_code range="1:" /> | 24 <exit_code range="1:" /> |
| 17 <exit_code range=":-1" /> | 25 <exit_code range=":-1" /> |
| 67 <when value="none" /><!-- no further questions --> | 75 <when value="none" /><!-- no further questions --> |
| 68 </conditional> | 76 </conditional> |
| 69 <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)" | 77 <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)" |
| 70 help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." /> | 78 help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." /> |
| 71 </repeat> | 79 </repeat> |
| 80 <param name="maf_wanted" type="boolean" label="Output mapping in MIRA's own format?" checked="False" /> | |
| 81 <param name="bam_wanted" type="boolean" label="Convert mapping into BAM format?" checked="True" /> | |
| 72 </inputs> | 82 </inputs> |
| 73 <outputs> | 83 <outputs> |
| 74 <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" /> | 84 <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" /> |
| 75 <data name="out_bam" format="bam" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly (BAM)" /> | 85 <data name="out_bam" format="bam" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly (BAM)"> |
| 76 <data name="out_maf" format="mira" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly" /> | 86 <filter>bam_wanted is True</filter> |
| 87 </data> | |
| 88 <data name="out_maf" format="mira" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly"> | |
| 89 <filter>maf_wanted is True</filter> | |
| 90 </data> | |
| 77 <data name="out_log" format="txt" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping log" /> | 91 <data name="out_log" format="txt" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping log" /> |
| 78 </outputs> | 92 </outputs> |
| 79 <configfiles> | 93 <configfiles> |
| 80 <configfile name="manifest"> | 94 <configfile name="manifest"> |
| 81 project = MIRA | 95 project = MIRA |
| 166 <param name="job_quality" value="accurate" /> | 180 <param name="job_quality" value="accurate" /> |
| 167 <param name="references" value="tvc_contigs.fasta" ftype="fasta" /> | 181 <param name="references" value="tvc_contigs.fasta" ftype="fasta" /> |
| 168 <param name="strain_setup" value="default" /> | 182 <param name="strain_setup" value="default" /> |
| 169 <param name="type" value="none" /> | 183 <param name="type" value="none" /> |
| 170 <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" /> | 184 <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" /> |
| 185 <param name="maf_wanted" value="true"/> | |
| 186 <param name="bam_wanted" value="true"/> | |
| 171 <output name="out_fasta" file="tvc_map_ref_strain.fasta" ftype="fasta" /> | 187 <output name="out_fasta" file="tvc_map_ref_strain.fasta" ftype="fasta" /> |
| 172 <output name="out_bam" file="empty_file.dat" compare="contains" /> | 188 <output name="out_bam" file="empty_file.dat" compare="contains" /> |
| 173 <output name="out_maf" file="empty_file.dat" compare="contains" /> | 189 <output name="out_maf" file="empty_file.dat" compare="contains" /> |
| 174 <output name="out_log" file="empty_file.dat" compare="contains" /> | 190 <output name="out_log" file="empty_file.dat" compare="contains" /> |
| 175 </test> | 191 </test> |
| 178 <param name="job_quality" value="accurate" /> | 194 <param name="job_quality" value="accurate" /> |
| 179 <param name="references" value="tvc_contigs.fasta" ftype="fasta" /> | 195 <param name="references" value="tvc_contigs.fasta" ftype="fasta" /> |
| 180 <param name="strain_setup" value="same" /> | 196 <param name="strain_setup" value="same" /> |
| 181 <param name="type" value="none" /> | 197 <param name="type" value="none" /> |
| 182 <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" /> | 198 <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" /> |
| 199 <param name="maf_wanted" value="true"/> | |
| 200 <param name="bam_wanted" value="true"/> | |
| 183 <output name="out_fasta" file="tvc_map_same_strain.fasta" ftype="fasta" /> | 201 <output name="out_fasta" file="tvc_map_same_strain.fasta" ftype="fasta" /> |
| 184 <output name="out_bam" file="empty_file.dat" compare="contains" /> | 202 <output name="out_bam" file="empty_file.dat" compare="contains" /> |
| 185 <output name="out_maf" file="empty_file.dat" compare="contains" /> | 203 <output name="out_maf" file="empty_file.dat" compare="contains" /> |
| 186 <output name="out_log" file="empty_file.dat" compare="contains" /> | 204 <output name="out_log" file="empty_file.dat" compare="contains" /> |
| 187 </test> | 205 </test> |