Mercurial > repos > saskia-hiltemann > cgatools_v17

changeset 14:59a2f9ad76dd draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 4df562cd801221f33652de8b8b4dbbf41deea8ea-dirty
author yhoogstrate
date Tue, 17 Nov 2015 04:43:00 -0500
parents ff641b41735f
children b5c879e950f5
files datatypes_conf.xml lib/galaxy/datatypes/completegenomics.py tools/cgatools17/listvariants_v17.xml tools/cgatools17/testvariants_v17.xml
diffstat 4 files changed, 15 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/datatypes_conf.xml	Wed Nov 11 04:59:04 2015 -0500
+++ b/datatypes_conf.xml	Tue Nov 17 04:43:00 2015 -0500
@@ -17,5 +17,6 @@
     <!-- End of copied section -->
   </registration>
   <sniffers>
+    <sniffer type="galaxy.datatypes.completegenomics:CRR"/>
   </sniffers>
 </datatypes>
--- a/lib/galaxy/datatypes/completegenomics.py	Wed Nov 11 04:59:04 2015 -0500
+++ b/lib/galaxy/datatypes/completegenomics.py	Tue Nov 17 04:43:00 2015 -0500
@@ -17,6 +17,7 @@
 from galaxy.datatypes.binary import Binary
 import galaxy_utils.sequence.vcf
 from galaxy.datatypes.sniff import *
+import binascii
 
 log = logging.getLogger(__name__)
 
@@ -98,5 +99,6 @@
         except:
             return False
 
+
 # Does not work for some reason - uploaded files keep receiving "The uploaded binary file contains inappropriate content"
 Binary.register_sniffable_binary_format('CRR', 'crr', CRR)
--- a/tools/cgatools17/listvariants_v17.xml	Wed Nov 11 04:59:04 2015 -0500
+++ b/tools/cgatools17/listvariants_v17.xml	Tue Nov 17 04:43:00 2015 -0500
@@ -13,10 +13,10 @@
             listvariants
             --beta
 
-            #if $reference_genome_source.source_select == "indexed_filtered"
-                ${reference_genome_source.crr.fields.crr_path}
-            #else if $reference_genome_source.source_select == "history"
-                ${reference_genome_source.crr}
+            #if $reference_gene_sets_source.source_select == "indexed_filtered"
+                ${reference_gene_sets_source.crr.fields.crr_path}
+            #else if $reference_gene_sets_source.source_select == "history"
+                ${reference_gene_sets_source.crr}
             #end if
             
             --output $output
@@ -33,8 +33,8 @@
 
     <inputs>
     <!--form field to select crr file-->
-        <conditional name="reference_genome_source">
-            <param name="source_select" type="select" label="CRR Genome reference Source">
+        <conditional name="reference_gene_sets_source">
+            <param name="source_select" type="select" label="GFF/GTF Source">
                 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
                 <option value="history">Use reference from the history</option>
             </param>
--- a/tools/cgatools17/testvariants_v17.xml	Wed Nov 11 04:59:04 2015 -0500
+++ b/tools/cgatools17/testvariants_v17.xml	Tue Nov 17 04:43:00 2015 -0500
@@ -12,10 +12,10 @@
         --beta
         --reference
         
-            #if $reference_genome_source.source_select == "indexed_filtered"
-                ${reference_genome_source.crr.fields.crr_path}
-            #else if $reference_genome_source.source_select == "history"
-                ${reference_genome_source.crr}
+            #if $reference_gene_sets_source.source_select == "indexed_filtered"
+                ${reference_gene_sets_source.crr.fields.crr_path}
+            #else if $reference_gene_sets_source.source_select == "history"
+                ${reference_gene_sets_source.crr}
             #end if
             
         --output $output
@@ -29,8 +29,8 @@
     <inputs>
     <!--form field to select crr file-->
     
-        <conditional name="reference_genome_source">
-            <param name="source_select" type="select" label="CRR Genome reference Source">
+        <conditional name="reference_gene_sets_source">
+            <param name="source_select" type="select" label="GFF/GTF Source">
                 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
                 <option value="history">Use reference from the history</option>
             </param>