# HG changeset patch
# User devteam
# Date 1486510742 18000
# Node ID f1b92120dfaa16dca13ff99dbcf40c9b7153b681
# Parent  0f32ad418df810666409db50f5f57202ca62b895
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f

diff -r 0f32ad418df8 -r f1b92120dfaa cuff_macros.xml
--- a/cuff_macros.xml	Wed Nov 11 12:34:34 2015 -0500
+++ b/cuff_macros.xml	Tue Feb 07 18:39:02 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>
diff -r 0f32ad418df8 -r f1b92120dfaa cuffdiff_wrapper.xml
--- a/cuffdiff_wrapper.xml	Wed Nov 11 12:34:34 2015 -0500
+++ b/cuffdiff_wrapper.xml	Tue Feb 07 18:39:02 2017 -0500
@@ -1,14 +1,12 @@
-<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.3">
+<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.4">
     <description>find significant changes in transcript expression, splicing, and promoter use</description>
-    <requirements>
-        <requirement type="set_environment">CUFFDIFF_SCRIPT_PATH</requirement>
-        <requirement type="package" version="2.2.1">cufflinks</requirement>
-        <requirement type="package" version="2.8.2">cummeRbund</requirement>
-    </requirements>
-    <expand macro="stdio" />
     <macros>
       <import>cuff_macros.xml</import>
     </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="2.8.2">bioconductor-cummerbund</requirement>
+    </expand>
+    <expand macro="stdio" />
     <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
     <command><![CDATA[
         cuffdiff
@@ -36,10 +34,10 @@
                -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
 
@@ -53,7 +51,7 @@
                         --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
                 #if $advanced_settings.time_series:
                         --time-series
@@ -66,12 +64,12 @@
                 --min-reps-for-js-test=$advanced_settings.min_reps_for_js_test
             #end if
             ## Inputs.
-            $gtf_input
+            '$gtf_input'
 
             @CONDITION_SAMPLES@
             #if $generate_sqlite:
                 &&
-                R --vanilla --no-save -f \$CUFFDIFF_SCRIPT_PATH/cummeRbund.R && mv cummeRbund.sqlite "${output_cummerbund}"
+                R --vanilla --no-save -f '$__tool_directory__/cummeRbund.R' && mv cummeRbund.sqlite '${output_cummerbund}'
             #end if
             ]]>
     </command>
@@ -276,15 +274,11 @@
                     <param name="set_in_type" value="BAM" />
                     <repeat name="conditions">
                         <param name="name" value="q1" />
-                        <repeat name="samples">
-                            <param name="sample" value="cuffdiff_in1.sam" ftype="sam" />
-                        </repeat>
+                        <param name="samples" value="cuffdiff_in1.sam" ftype="sam" />
                     </repeat>
                     <repeat name="conditions">
                         <param name="name" value="q2" />
-                        <repeat name="samples">
-                            <param name="sample" value="cuffdiff_in2.sam" ftype="sam" />
-                        </repeat>
+                        <param name="samples" value="cuffdiff_in2.sam" ftype="sam" />
                     </repeat>
                 </conditional>
                 <param name="fdr" value="0.05" />
@@ -293,7 +287,7 @@
                 <param name="do_normalization" value="No" />
                 <param name="multiread_correct" value="No"/>
                 <param name="sAdditional" value="No"/>
-                <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite"/>
+                <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />
         </test>
         <test>
                 <!--
@@ -305,15 +299,11 @@
                     <param name="set_in_type" value="BAM" />
                     <repeat name="conditions">
                         <param name="name" value="q1" />
-                        <repeat name="samples">
-                            <param name="sample" value="cuffdiff_in1.sam" ftype="sam" />
-                        </repeat>
+                        <param name="samples" value="cuffdiff_in1.sam" ftype="sam" />
                     </repeat>
                     <repeat name="conditions">
                         <param name="name" value="q2" />
-                        <repeat name="samples">
-                            <param name="sample" value="cuffdiff_in2.sam" ftype="sam" />
-                        </repeat>
+                        <param name="samples" value="cuffdiff_in2.sam" ftype="sam" />
                     </repeat>
                 </conditional>
                 <param name="fdr" value="0.05" />
diff -r 0f32ad418df8 -r f1b92120dfaa tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 11 12:34:34 2015 -0500
+++ b/tool_dependencies.xml	Tue Feb 07 18:39:02 2017 -0500
@@ -7,6 +7,6 @@
         <repository changeset_revision="899067a260d1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="cummeRbund" version="2.8.2">
-        <repository changeset_revision="13c270433440" name="package_cummerbund_2_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="754912f24120" name="package_cummerbund_2_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>