Repository 'cpt_convert_glimmer'
hg clone https://toolshed.g2.bx.psu.edu/repos/cpt/cpt_convert_glimmer

Changeset 3:061b5ee5b844 (2022-05-19)
Previous changeset 2:f62001b83a21 (2022-05-19) Next changeset 4:71c68eb1c30f (2022-05-20)
Commit message:
Uploaded
modified:
cpt_convert_glimmer/macros.xml
b
diff -r f62001b83a21 -r 061b5ee5b844 cpt_convert_glimmer/macros.xml
--- a/cpt_convert_glimmer/macros.xml Thu May 19 23:45:30 2022 +0000
+++ b/cpt_convert_glimmer/macros.xml Thu May 19 23:54:32 2022 +0000
b
@@ -9,20 +9,7 @@
  </requirements>
  </xml>
  <xml name="genome_selector">
- <conditional name="reference_genome">
- <param name="reference_genome_source" type="select" label="Reference Genome">
- <option value="history" selected="True">From History</option>
- <option value="cached">Locally Cached</option>
- </param>
- <when value="cached">
- <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
- <options from_data_table="all_fasta"/>
- </param>
- </when>
- <when value="history">
- <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
- </when>
- </conditional>
+ <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
  </xml>
  <xml name="gff3_input">
  <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
@@ -35,23 +22,13 @@
  "$gff3_data"
  </token>
  <token name="@INPUT_FASTA@">
-#if str($reference_genome.reference_genome_source) == 'cached':
- "${reference_genome.fasta_indexes.fields.path}"
-#else if str($reference_genome.reference_genome_source) == 'history':
  genomeref.fa
-#end if
  </token>
  <token name="@GENOME_SELECTOR_PRE@">
-#if $reference_genome.reference_genome_source == 'history':
- ln -s $reference_genome.genome_fasta genomeref.fa;
-#end if
+ ln -s $genome_fasta genomeref.fa;
  </token>
  <token name="@GENOME_SELECTOR@">
-#if str($reference_genome.reference_genome_source) == 'cached':
- "${reference_genome.fasta_indexes.fields.path}"
-#else if str($reference_genome.reference_genome_source) == 'history':
  genomeref.fa
-#end if
  </token>
         <xml name="input/fasta">
  <param label="Fasta file" name="sequences" type="data" format="fasta"/>