Mercurial > repos > iuc > rna_starsolo
comparison macros.xml @ 1:e613048778d9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f"
| author | iuc |
|---|---|
| date | Sat, 17 Aug 2019 09:37:54 -0400 |
| parents | e3c94e2933c9 |
| children | 3a1253ee137b |
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| 0:e3c94e2933c9 | 1:e613048778d9 |
|---|---|
| 19 <requirement type="package" version="@VERSION@">star</requirement> | 19 <requirement type="package" version="@VERSION@">star</requirement> |
| 20 <requirement type="package" version="1.9">samtools</requirement> | 20 <requirement type="package" version="1.9">samtools</requirement> |
| 21 </requirements> | 21 </requirements> |
| 22 </xml> | 22 </xml> |
| 23 | 23 |
| 24 <xml name="index_selection" token_with_gene_model="1"> | 24 <xml name="index_selection" token_with_gene_model="0"> |
| 25 <param argument="--genomeDir" name="genomeDir" type="select" | 25 <param argument="--genomeDir" name="genomeDir" type="select" |
| 26 label="Select reference genome" | 26 label="Select reference genome" |
| 27 help="If your genome of interest is not listed, contact the Galaxy team"> | 27 help="If your genome of interest is not listed, contact the Galaxy team"> |
| 28 <options from_data_table="rnastar_index2_versioned"> | 28 <options from_data_table="rnastar_index2_versioned"> |
| 29 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" /> | 29 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" /> |
| 125 <when value="indexed"> | 125 <when value="indexed"> |
| 126 <conditional name="GTFconditional"> | 126 <conditional name="GTFconditional"> |
| 127 <param name="GTFselect" type="select" | 127 <param name="GTFselect" type="select" |
| 128 label="Reference genome with or without an annotation" | 128 label="Reference genome with or without an annotation" |
| 129 help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions."> | 129 help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions."> |
| 130 <option value="without-gtf">use genome reference with builtin gene-model</option> | 130 <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option> |
| 131 <option value="with-gtf">use genome reference without builtin gene-model</option> | 131 <option value="with-gtf">use genome reference with builtin gene-model</option> |
| 132 </param> | 132 </param> |
| 133 <when value="with-gtf"> | 133 <when value="with-gtf"> |
| 134 <expand macro="index_selection" with_gene_model="0" /> | 134 <expand macro="index_selection" with_gene_model="1" /> |
| 135 <expand macro="@SJDBOPTIONS@" /> | 135 <expand macro="@SJDBOPTIONS@" /> |
| 136 </when> | 136 </when> |
| 137 <when value="without-gtf"> | 137 <when value="without-gtf"> |
| 138 <expand macro="index_selection" with_gene_model="1" /> | 138 <expand macro="index_selection" with_gene_model="0" /> |
| 139 </when> | 139 </when> |
| 140 </conditional> | 140 </conditional> |
| 141 </when> | 141 </when> |
| 142 <when value="history"> | 142 <when value="history"> |
| 143 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" /> | 143 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" /> |