Mercurial > repos > chrisw > monorail_test
comparison monorail.xml @ 24:d16b3dc144d8 draft
Uploaded
| author | chrisw |
|---|---|
| date | Thu, 14 Nov 2019 06:09:46 +0000 |
| parents | 7f26c88a86d7 |
| children | 2b6bfe0e2127 |
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| 23:7f26c88a86d7 | 24:d16b3dc144d8 |
|---|---|
| 32 #end if | 32 #end if |
| 33 #if $singlePaired.input1.is_of_type("fastq.gz"): | 33 #if $singlePaired.input1.is_of_type("fastq.gz"): |
| 34 compressed=1 | 34 compressed=1 |
| 35 #end if | 35 #end if |
| 36 #end if | 36 #end if |
| 37 ref="$refGenomeSource.genomeDir.fields.path" | 37 ref="$index_source.fields.path" |
| 38 output="." | 38 output="." |
| 39 temp="./tmp" | 39 temp="./tmp" |
| 40 ]]></command> | 40 ]]></command> |
| 41 <inputs> | 41 <inputs> |
| 42 <!-- FASTQ input(s) and options specifically for paired-end data. --> | 42 <!-- FASTQ input(s) and options specifically for paired-end data. --> |
| 67 </options> | 67 </options> |
| 68 </param> | 68 </param> |
| 69 --> | 69 --> |
| 70 | 70 |
| 71 <!-- Genome source. --> | 71 <!-- Genome source. --> |
| 72 <conditional name="refGenomeSource"> | 72 <param name="index_source" type="select" label="Select reference genome index set" help="If your genome of interest is not listed, contact the Galaxy team"> |
| 73 <param name="genomeDir" type="select" label="Select reference genome index set" help="If your genome of interest is not listed, contact the Galaxy team"> | |
| 74 <options from_data_table="rnastar_index2_versioned"> | 73 <options from_data_table="rnastar_index2_versioned"> |
| 75 <filter type="sort_by" column="2" /> | 74 <filter type="sort_by" column="2" /> |
| 76 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | 75 <validator type="no_options" message="No indexes are available for the selected input dataset"/> |
| 77 </options> | 76 </options> |
| 78 </param> | 77 </param> |
| 79 </conditional> | |
| 80 </inputs> | 78 </inputs> |
| 81 <outputs> | 79 <outputs> |
| 82 <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bamcount_auc.tsv"/> | 80 <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bamcount_auc.tsv"/> |
| 83 <!-- | 81 <!-- |
| 84 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/> | 82 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/> |