diff circgraph.xml @ 6:169adf243c0a draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec

--- a/circgraph.xml	Sat Jun 10 12:55:28 2017 -0400
+++ b/circgraph.xml	Sat Jun 10 13:38:32 2017 -0400
@@ -14,20 +14,23 @@
         ln -s $reference_genome.genome_fasta genomeref.fa;
     #end if
 
-    ## Process the karyotype.txt file
-    python $__tool_directory__/fasta-to-karyotype.py
+    #if $reference_genome.reference_genome_source != 'karyotype':
+        ## Process the karyotype.txt file
+        python $__tool_directory__/fasta-to-karyotype.py
 
-        #if str($reference_genome.reference_genome_source) == 'cached':
-            "${reference_genome.fasta_indexes.fields.path}"
-        #else if str($reference_genome.reference_genome_source) == 'history':
-            genomeref.fa
-        #end if
+            #if str($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
 
-        #if $ideogram.bands:
-            "${ideogram.bands}"
-        #end if
-
-    > circos/conf/karyotype.txt &&
+            #if $ideogram.bands:
+                "${ideogram.bands}"
+            #end if
+        > circos/conf/karyotype.txt &&
+    #else
+        cp $reference_genome.input_karyotype circos/conf/karyotype.txt &&
+    #end if
 
     mv $circos_conf circos/conf/circos.conf &&
     mv $ticks_conf circos/conf/ticks.conf &&
@@ -82,14 +85,24 @@
         <param name="reference_genome_source" type="select" label="Reference Genome">
             <option value="history" selected="True">From History</option>
             <option value="cached">Locally Cached</option>
+            <option value="karyotype">Karyotype</option>
         </param>
         <when value="cached">
             <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
                 <options from_data_table="all_fasta"/>
             </param>
+            <!-- TODO: multiple band files? -->
+            <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
+                   help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
         </when>
         <when value="history">
             <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
+            <!-- TODO: multiple band files? -->
+            <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
+                   help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
+        </when>
+        <when value="karyotype">
+            <param name="input_karyotype" type="data" format="tabular,txt" label="Karyotype Configuration"/>
         </when>
     </conditional>
 
@@ -105,9 +118,6 @@
             <param name="parallel" type="boolean" label="Parallel" truevalue="yes" falsevalue="no"
                  help="When set to yes/true, labels will be perpendicular to the tangent of the circle at the location of the label. Otherwise, they will be parallel with the tangent of the circle"/>
         </section>
-        <!-- TODO: multiple band files? -->
-        <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
-             help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
     </section>
 
     <section name="ticks" title="Ticks">