Mercurial > repos > peterjc > mira_assembler
comparison tools/mira3/mira.xml @ 11:e59904c855ae draft
Uploaded v0.0.10, adds a test and updated download URL
| author | peterjc |
|---|---|
| date | Wed, 30 Apr 2014 07:21:57 -0400 |
| parents | a2fb1e67bd11 |
| children | 63ebe9726219 |
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| 10:a2fb1e67bd11 | 11:e59904c855ae |
|---|---|
| 1 <tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.8"> | 1 <tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.10"> |
| 2 <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description> | 2 <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="binary">mira</requirement> | 4 <requirement type="binary">mira</requirement> |
| 5 <requirement type="package" version="3.4.1.1">MIRA</requirement> | 5 <requirement type="package" version="3.4.1.1">MIRA</requirement> |
| 6 </requirements> | 6 </requirements> |
| 70 <option value="normal">Normal (deprecated)</option> | 70 <option value="normal">Normal (deprecated)</option> |
| 71 <option value="draft">Draft</option> | 71 <option value="draft">Draft</option> |
| 72 </param> | 72 </param> |
| 73 <!-- Backbone --> | 73 <!-- Backbone --> |
| 74 <conditional name="condBackbone"> | 74 <conditional name="condBackbone"> |
| 75 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly."> | 75 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly."> |
| 76 <option value="false">No</option> | 76 <option value="false">No</option> |
| 77 <option value="true">Yes</option> | 77 <option value="true">Yes</option> |
| 78 </param> | 78 </param> |
| 79 <when value="false" /> | 79 <when value="false" /> |
| 80 <when value="true"> | 80 <when value="true"> |
| 81 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) --> | 81 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) --> |
| 82 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" /> | 82 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" /> |
| 83 </when> | 83 </when> |
| 84 </conditional> | 84 </conditional> |
| 85 <!-- Sanger --> | 85 <!-- Sanger --> |
| 86 <conditional name="condSanger"> | 86 <conditional name="condSanger"> |
| 87 <param name="use" type="select" label="Sanger/Capillary reads?"> | 87 <param name="use" type="select" label="Sanger/Capillary reads?"> |
| 88 <option value="false">No</option> | 88 <option value="false">No</option> |
| 89 <option value="true">Yes</option> | 89 <option value="true">Yes</option> |
| 90 </param> | 90 </param> |
| 91 <when value="false" /> | 91 <when value="false" /> |
| 92 <when value="true"> | 92 <when value="true"> |
| 93 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" /> | 93 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" /> |
| 94 </when> | 94 </when> |
| 95 </conditional> | 95 </conditional> |
| 96 <!-- Roche 454 --> | 96 <!-- Roche 454 --> |
| 97 <conditional name="condRoche"> | 97 <conditional name="condRoche"> |
| 98 <param name="use" type="select" label="454 reads?"> | 98 <param name="use" type="select" label="454 reads?"> |
| 99 <option value="false">No</option> | 99 <option value="false">No</option> |
| 100 <option value="true">Yes</option> | 100 <option value="true">Yes</option> |
| 101 </param> | 101 </param> |
| 102 <when value="false" /> | 102 <when value="false" /> |
| 103 <when value="true"> | 103 <when value="true"> |
| 104 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences --> | 104 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences --> |
| 105 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" /> | 105 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" /> |
| 106 </when> | 106 </when> |
| 107 </conditional> | 107 </conditional> |
| 108 <!-- Illumina --> | 108 <!-- Illumina --> |
| 109 <conditional name="condIllumina"> | 109 <conditional name="condIllumina"> |
| 110 <param name="use" type="select" label="Solexa/Illumina reads?"> | 110 <param name="use" type="select" label="Solexa/Illumina reads?"> |
| 111 <option value="false">No</option> | 111 <option value="false">No</option> |
| 112 <option value="true">Yes</option> | 112 <option value="true">Yes</option> |
| 113 </param> | 113 </param> |
| 114 <when value="false" /> | 114 <when value="false" /> |
| 115 <when value="true"> | 115 <when value="true"> |
| 116 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" /> | 116 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" /> |
| 117 </when> | 117 </when> |
| 118 </conditional> | 118 </conditional> |
| 119 <!-- Ion Torrent --> | 119 <!-- Ion Torrent --> |
| 120 <conditional name="condIonTorrent"> | 120 <conditional name="condIonTorrent"> |
| 121 <param name="use" type="select" label="Ion Torrent reads?"> | 121 <param name="use" type="select" label="Ion Torrent reads?"> |
| 122 <option value="false">No</option> | 122 <option value="false">No</option> |
| 123 <option value="true">Yes</option> | 123 <option value="true">Yes</option> |
| 124 </param> | 124 </param> |
| 125 <when value="false" /> | 125 <when value="false" /> |
| 126 <when value="true"> | 126 <when value="true"> |
| 127 <!-- TODO? Support SFF files directly, e.g. with sff_extract --> | 127 <!-- TODO? Support SFF files directly, e.g. with sff_extract --> |
| 128 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" /> | 128 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" /> |
| 129 </when> | 129 </when> |
| 130 </conditional> | 130 </conditional> |
| 131 </inputs> | 131 </inputs> |
| 132 <outputs> | 132 <outputs> |
| 133 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" /> | 133 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" /> |
| 134 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" /> | 134 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" /> |
| 136 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" /> | 136 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" /> |
| 137 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> | 137 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> |
| 138 <data name="out_log" format="txt" label="MIRA log" /> | 138 <data name="out_log" format="txt" label="MIRA log" /> |
| 139 </outputs> | 139 </outputs> |
| 140 <tests> | 140 <tests> |
| 141 <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses | 141 <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses |
| 142 strain data and miraSearchESTSNPs. Here we just assemble it. --> | 142 strain data and miraSearchESTSNPs. Here we just assemble it. --> |
| 143 <!-- | |
| 144 Commenting out test until Galaxy framework is fixed, | |
| 145 https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests | |
| 146 <test> | 143 <test> |
| 147 <param name="job_method" value="denovo" /> | 144 <param name="job_method" value="denovo" /> |
| 148 <param name="job_type" value="est" /> | 145 <param name="job_type" value="est" /> |
| 149 <param name="job_qual" value="accurate" /> | 146 <param name="job_qual" value="accurate" /> |
| 150 <param name="condBackbone.use" value="false" /> | 147 <param name="condBackbone|use" value="false" /> |
| 151 <param name="condSanger.use" value="true" /> | 148 <param name="condSanger|use" value="true" /> |
| 152 <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" /> | 149 <param name="condSanger|filename" value="tvc_mini.fastq" ftype="fastq" /> |
| 153 <param name="condRoche.use" value="false" /> | 150 <param name="condRoche|use" value="false" /> |
| 154 <param name="condIllumina.use" value="false" /> | 151 <param name="condIllumina|use" value="false" /> |
| 155 <param name="condIonTorrent.use" value="false" /> | 152 <param name="condIonTorrent|use" value="false" /> |
| 156 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" /> | 153 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" /> |
| 157 </test> | 154 <output name="out_qual" file="empty_file.dat" compare="contains" /> |
| 158 --> | 155 <output name="out_caf" file="empty_file.dat" compare="contains" /> |
| 156 <output name="out_ace" file="empty_file.dat" compare="contains" /> | |
| 157 <output name="out_wig" file="empty_file.dat" compare="contains" /> | |
| 158 <output name="out_log" file="empty_file.dat" compare="contains" /> | |
| 159 </test> | |
| 159 </tests> | 160 </tests> |
| 160 <help> | 161 <help> |
| 161 | 162 |
| 162 **What it does** | 163 **What it does** |
| 163 | 164 |