changeset 2:885314f0d369 draft

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

--- a/cuff_macros.xml	Tue Oct 13 12:38:19 2015 -0400
+++ b/cuff_macros.xml	Tue Feb 07 18:39:20 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/cuffnorm_wrapper.xml	Tue Oct 13 12:38:19 2015 -0400
+++ b/cuffnorm_wrapper.xml	Tue Feb 07 18:39:20 2017 -0500
@@ -1,10 +1,10 @@
 <tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.1">
     <description>Create normalized expression levels</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
     <macros>
       <import>cuff_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <version_command>cuffnorm 2>&amp;1 | head -n 1</version_command>
     <command>
         cuffnorm
@@ -42,7 +42,7 @@
             <option value="Yes">Yes</option>
         </param>
 
-        <param name="output_format" type="select" lable="Output format" 
+        <param name="output_format" type="select" label="Output format" 
             help="By default, Cuffnorm reports expression levels in the 'simple-table' tab-delimted text files. The program also reports information about your samples and about the genes, transcripts, TSS groups, and CDS groups as tab delimited text files. Note that these files have a different format than the files used by Cuffdiff. However, you can direct Cuffnorm to report its output in the same format as used by Cuffdiff if you wish" >
                 <option value="simple-table" selected="True">Simple Table</option>
                 <option value="cuffdiff">Cuffdiff format</option>
@@ -166,12 +166,12 @@
         </data>
     </outputs>
     <tests>
+        <!-- 
         <test>
-            <!-- 
                 NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat
                 element are not supported.
-            -->
         </test>
+        -->
     </tests>
 
     <help>

--- a/tool_dependencies.xml	Tue Oct 13 12:38:19 2015 -0400
+++ b/tool_dependencies.xml	Tue Feb 07 18:39:20 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>