Mercurial > repos > peterjc > mira_assembler
comparison tools/mira3/mira.xml @ 25:56dede4f0735 draft
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira3/ commit 9526de68e38a82bb84b2d9267a8c290c6adcaa65
| author | peterjc |
|---|---|
| date | Fri, 15 Sep 2017 10:08:39 -0400 |
| parents | 83a94a5038a7 |
| children | 2e7e2bc0d718 |
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| 24:ad14a345f1b0 | 25:56dede4f0735 |
|---|---|
| 52 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 | 52 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 |
| 53 | 53 |
| 54 ##remove_rollover_tmps, remove_tmp_directory | 54 ##remove_rollover_tmps, remove_tmp_directory |
| 55 -OUT:rrot=1:rtd=1 | 55 -OUT:rrot=1:rtd=1 |
| 56 | 56 |
| 57 ##put mira temp directory on local storage | 57 ##put mira temp directory on local storage |
| 58 -DI:trt=/tmp | 58 -DI:trt=/tmp |
| 59 | 59 |
| 60 </command> | 60 </command> |
| 61 <inputs> | 61 <inputs> |
| 62 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)"> | 62 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)"> |
| 139 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> | 139 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> |
| 140 <data name="out_log" format="txt" label="MIRA log" /> | 140 <data name="out_log" format="txt" label="MIRA log" /> |
| 141 </outputs> | 141 </outputs> |
| 142 <tests> | 142 <tests> |
| 143 <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses | 143 <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses |
| 144 strain data and miraSearchESTSNPs. Here we just assemble it. --> | 144 strain data and miraSearchESTSNPs. Here we just assemble it. --> |
| 145 <test> | 145 <test> |
| 146 <param name="job_method" value="denovo" /> | 146 <param name="job_method" value="denovo" /> |
| 147 <param name="job_type" value="est" /> | 147 <param name="job_type" value="est" /> |
| 148 <param name="job_qual" value="accurate" /> | 148 <param name="job_qual" value="accurate" /> |
| 149 <param name="condBackbone|use" value="false" /> | 149 <param name="condBackbone|use" value="false" /> |
| 150 <param name="condSanger|use" value="true" /> | 150 <param name="condSanger|use" value="true" /> |
| 151 <param name="condSanger|filename" value="tvc_mini.fastq" ftype="fastq" /> | 151 <param name="condSanger|filename" value="tvc_mini.fastq" ftype="fastq" /> |
| 152 <param name="condRoche|use" value="false" /> | 152 <param name="condRoche|use" value="false" /> |
| 153 <param name="condIllumina|use" value="false" /> | 153 <param name="condIllumina|use" value="false" /> |
| 154 <param name="condIonTorrent|use" value="false" /> | 154 <param name="condIonTorrent|use" value="false" /> |
| 155 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" /> | 155 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" /> |
| 156 <output name="out_qual" file="empty_file.dat" compare="contains" /> | 156 <output name="out_qual" file="empty_file.dat" compare="contains" /> |
| 157 <output name="out_caf" file="empty_file.dat" compare="contains" /> | 157 <output name="out_caf" file="empty_file.dat" compare="contains" /> |
| 158 <output name="out_ace" file="empty_file.dat" compare="contains" /> | 158 <output name="out_ace" file="empty_file.dat" compare="contains" /> |
| 186 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. | 186 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. |
| 187 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. | 187 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. |
| 188 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html | 188 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html |
| 189 | 189 |
| 190 This wrapper is available to install into other Galaxy Instances via the Galaxy | 190 This wrapper is available to install into other Galaxy Instances via the Galaxy |
| 191 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler | 191 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler |
| 192 | 192 |
| 193 </help> | 193 </help> |
| 194 <citations> | 194 <citations> |
| 195 <citation type="doi">10.7717/peerj.167</citation> | 195 <citation type="doi">10.7717/peerj.167</citation> |
| 196 <citation type="bibtex">@ARTICLE{Chevreux1999-mira3, | 196 <citation type="bibtex">@ARTICLE{Chevreux1999-mira3, |