Mercurial > repos > romaingred > pirna_pipeline
changeset 34:02c46c8164a8 draft
Uploaded
| author | romaingred |
|---|---|
| date | Tue, 28 Nov 2017 09:08:28 -0500 |
| parents | 46d7549c1a05 |
| children | 67edc34cf0ef |
| files | piPipe.xml |
| diffstat | 1 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/piPipe.xml Tue Nov 28 09:08:13 2017 -0500 +++ b/piPipe.xml Tue Nov 28 09:08:28 2017 -0500 @@ -39,11 +39,11 @@ --miRNAs "${miRNAs.indices.fields.path}" #end if - #if $exons.refGenomeSource == "history": - --exons "${exons.ownFile}" - --build_exons + #if $transcripts.refGenomeSource == "history": + --transcripts "${transcripts.ownFile}" + --build_transcripts #else: - --exons "${exons.indices.fields.path}" + --transcripts "${transcripts.indices.fields.path}" #end if #if $TE.refGenomeSource == "history": @@ -187,13 +187,13 @@ <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> </when> </conditional> - <conditional name="exons"> - <param name="refGenomeSource" type="select" label="Will you select exons database from your history or use a built-in index?"> + <conditional name="transcripts"> + <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> </param> <when value="indexed"> - <param name="indices" type="select" label="Select a exons reference"> + <param name="indices" type="select" label="Select a transcripts reference"> <options from_data_table="bwa_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" />