changeset 3:25cf1ab351df draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit eb18f691975ef9539b5ebd4f118343c8ad967a1f

--- a/cuff_macros.xml	Mon Nov 09 12:06:19 2015 -0500
+++ b/cuff_macros.xml	Tue Feb 07 18:39:37 2017 -0500
@@ -1,11 +1,13 @@
 <macros>
   <token name="@VERSION@">2.2.1</token>
+
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="2.2.1">cufflinks</requirement>
       <yield />
     </requirements>
   </xml>
+
   <xml name="stdio">
     <stdio>
         <exit_code range="1:" />
@@ -26,21 +28,21 @@
         </param>
         <when value="BAM">
             <repeat name="conditions" title="Condition" min="2">
-                <param name="name" title="Condition name" type="text" label="Name"/>
+                <param name="name" label="Condition name" type="text"/>
                 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>
             </repeat>
         </when>
         <when value="CXB">
             <repeat name="conditions" title="Condition" min="2">
-                <param name="name" title="Condition name" type="text" label="Name"/>
+                <param name="name" label="Condition name" type="text"/>
                 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>
             </repeat>
         </when>
         <when value="CONDITION_LIST">
-            <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list" />
+            <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
         </when>
         <when value="CONDITION_REPLICATE_LIST">
-            <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" />
+            <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />
         </when>
     </conditional>
   </xml>
@@ -48,16 +50,16 @@
             #if $in_type.set_in_type in ['BAM', 'CXB']
                 #for $condition in $in_type.conditions:
                     #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] )
-                    $samples
+                    '$samples'
                 #end for
             #elif $in_type.set_in_type == 'CONDITION_LIST'
                 #for $sample in $in_type.conditions:
-                    $sample
+                    '$sample'
                 #end for
             #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
                 #for $condition_list in $in_type.conditions:
                     #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] )
-                    $samples
+                    '$samples'
                 #end for
             #end if
   </token>
@@ -79,11 +81,11 @@
   <token name="@CUFFLINKS_GTF_INPUTS@">
             ## Inputs.
             #for $input_file in $inputs:
-                "${input_file}"
+                '${input_file}'
             #end for
             #for $additional_input in $additional_inputs:
                 #for $input_file in $additional_input.additional_inputs:
-                  "${input_file}"
+                    '${input_file}'
                 #end for
             #end for
   </token>

--- a/cuffquant_wrapper.xml	Mon Nov 09 12:06:19 2015 -0500
+++ b/cuffquant_wrapper.xml	Tue Feb 07 18:39:37 2017 -0500
@@ -1,11 +1,11 @@
 <tool id="cuffquant" name="Cuffquant" version="@VERSION@.0">
     <!-- Wrapper supports Cuffdiff versions 2.2.1 -->
     <description>Precompute gene expression levels</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
     <macros>
       <import>cuff_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <version_command>cuffquant 2>&amp;1 | head -n 1</version_command>
     <command>
         cuffquant
@@ -27,10 +27,10 @@
                -b
                 #if $bias_correction.seq_source.index_source == "history":
                     ## Custom genome from history.
-                    $bias_correction.seq_source.ref_file
+                    '$bias_correction.seq_source.ref_file'
                 #else:
                     ## Built-in genome.
-                     "${ bias_correction.seq_source.index.fields.path }"
+                    '${bias_correction.seq_source.index.fields.path}'
                 #end if
             #end if
 
@@ -42,15 +42,15 @@
                     --library-type=$advanced_settings.library_type
                 #end if
                 #if $advanced_settings.mask_file:
-                    --mask-file=$advanced_settings.mask_file
+                    --mask-file '$advanced_settings.mask_file'
                 #end if
                 --max-mle-iterations=$advanced_settings.max_mle_iterations
                 --max-bundle-frags=$advanced_settings.max_bundle_frags
             #end if
             ## Inputs.
-            $gtf_input
+            '$gtf_input'
             #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] )
-            $samplestring
+            '$samplestring'
     </command>
     <inputs>
         <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts"

--- a/tool_dependencies.xml	Mon Nov 09 12:06:19 2015 -0500
+++ b/tool_dependencies.xml	Tue Feb 07 18:39:37 2017 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="cufflinks" version="2.2.1">
-        <repository changeset_revision="8f755957b6a1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="87f239da61af" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>