Mercurial > repos > yating-l > jbrowse_hub
comparison jbrowse_hub.xml @ 15:8627394693c6 draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
| author | yating-l |
|---|---|
| date | Tue, 14 Mar 2017 14:57:39 -0400 |
| parents | 0e29c929a8ee |
| children | 99d66676570b |
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| 14:0e29c929a8ee | 15:8627394693c6 |
|---|---|
| 26 #end if | 26 #end if |
| 27 #if $f.formatChoice.format_select == 'bam' | 27 #if $f.formatChoice.format_select == 'bam' |
| 28 --bam $f.formatChoice.BAM | 28 --bam $f.formatChoice.BAM |
| 29 #end if | 29 #end if |
| 30 #if $f.formatChoice.format_select == 'gff3_transcript' | 30 #if $f.formatChoice.format_select == 'gff3_transcript' |
| 31 --gff3_transcript $f.formatChoice.GFF3-transcript | 31 --gff3_transcript $f.formatChoice.GFF3_transcript |
| 32 #end if | 32 #end if |
| 33 #if $f.formatChoice.format_select == 'gff3_mrna' | 33 #if $f.formatChoice.format_select == 'gff3_mrna' |
| 34 --gff3_mrna $f.formatChoice.GFF3-mrna | 34 --gff3_mrna $f.formatChoice.GFF3_mrna |
| 35 #end if | 35 #end if |
| 36 #if $f.formatChoice.format_select == 'blastxml' | 36 #if $f.formatChoice.format_select == 'blastxml' |
| 37 --blastxml $f.formatChoice.BlastXML | 37 --blastxml $f.formatChoice.BlastXML |
| 38 #end if | 38 #end if |
| 39 #if $f.formatChoice.format_select == 'gtf' | 39 #if $f.formatChoice.format_select == 'gtf' |
| 112 /> | 112 /> |
| 113 </when> | 113 </when> |
| 114 <when value="gff3_transcript"> | 114 <when value="gff3_transcript"> |
| 115 <param | 115 <param |
| 116 format="gff3" | 116 format="gff3" |
| 117 name="GFF3-transcript" | 117 name="GFF3_transcript" |
| 118 type="data" | 118 type="data" |
| 119 label="GFF3 File" | 119 label="GFF3 File" |
| 120 /> | 120 /> |
| 121 </when> | 121 </when> |
| 122 <when value="gff3_mrna"> | 122 <when value="gff3_mrna"> |
| 123 <param | 123 <param |
| 124 format="gff3" | 124 format="gff3" |
| 125 name="GFF3-mrna" | 125 name="GFF3_mrna" |
| 126 type="data" | 126 type="data" |
| 127 label="GFF3 File" | 127 label="GFF3 File" |
| 128 /> | 128 /> |
| 129 </when> | 129 </when> |
| 130 <when value="gtf"> | 130 <when value="gtf"> |
| 146 <test> | 146 <test> |
| 147 <param name="reference" value="dbia3/raw/dbia3.fa" /> | 147 <param name="reference" value="dbia3/raw/dbia3.fa" /> |
| 148 <param name="output" value="hubtest" /> | 148 <param name="output" value="hubtest" /> |
| 149 <repeat name="format"> | 149 <repeat name="format"> |
| 150 <conditional name="formatChoice"> | 150 <conditional name="formatChoice"> |
| 151 <param name="format_select" value="gff3"/> | 151 <param name="format_select" value="gff3_transcript"/> |
| 152 <param name="GFF3-transcript" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" /> | 152 <param name="GFF3_transcript" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" /> |
| 153 </conditional> | 153 </conditional> |
| 154 </repeat> | 154 </repeat> |
| 155 <output name="output" file="hubtest" > | 155 <output name="output" file="hubtest" > |
| 156 </output> | 156 </output> |
| 157 </test> | 157 </test> |