# HG changeset patch
# User iuc
# Date 1592326802 14400
# Node ID 43b36b3d4333e254e7a62ff6726ce3e19ec60f70
# Parent  d3ae7d9c22023e931ca3fecf17733b106bdbd182
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"

diff -r d3ae7d9c2202 -r 43b36b3d4333 cuff_macros.xml
--- a/cuff_macros.xml	Sun Feb 19 12:12:17 2017 -0500
+++ b/cuff_macros.xml	Tue Jun 16 13:00:02 2020 -0400
@@ -66,20 +66,26 @@
   </token>
   <xml name="cufflinks_gtf_inputs">
     <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
-    <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)">
-      <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" />
-    </repeat>
   </xml>
+  <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[
+            ## Inputs.
+            #for $i, $input_file in enumerate($inputs):
+                ln -s '${input_file}' input_$i &&
+            #end for
+  ]]></token>
   <token name="@CUFFLINKS_GTF_INPUTS@">
             ## Inputs.
-            #for $input_file in $inputs:
-                '${input_file}'
-            #end for
-            #for $additional_input in $additional_inputs:
-                #for $input_file in $additional_input.additional_inputs:
-                    '${input_file}'
-                #end for
+            #for $i, $input_file in enumerate($inputs):
+                'input_$i'
             #end for
   </token>
   <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
+
+  <xml name="citations">
+    <citations>
+        <citation type="doi">10.1038/nbt.1621</citation>
+        <yield/>
+    </citations>
+  </xml>
+
 </macros>
diff -r d3ae7d9c2202 -r 43b36b3d4333 cuffdiff_wrapper.xml
--- a/cuffdiff_wrapper.xml	Sun Feb 19 12:12:17 2017 -0500
+++ b/cuffdiff_wrapper.xml	Tue Jun 16 13:00:02 2020 -0400
@@ -1,12 +1,12 @@
 <tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.5">
     <description>find significant changes in transcript expression, splicing, and promoter use</description>
     <macros>
-      <import>cuff_macros.xml</import>
+        <import>cuff_macros.xml</import>
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="2.16.0">bioconductor-cummerbund</requirement>
     </expand>
-    <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
+    <version_command><![CDATA[cuffdiff 2>&1 | head -n 1]]></version_command>
     <command detect_errors="aggressive"><![CDATA[
         cuffdiff
             --no-update-check
@@ -175,8 +175,8 @@
                     help="Instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. Samples should be provided in increasing time order at the command line (e.g first time point SAM, second timepoint SAM, etc.)" />
                 <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" />
                 <param name="hits_norm" type="select" label="Hits included in normalization" help="All Hits: With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator. Compatible Hits: With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes. It is active by default." >
-                        <option value="--compatible-hits-norm" selected="True">Compatible Hits</option>
-                        <option value="--total-hits-norm">All Hits</option>
+                    <option value="--compatible-hits-norm" selected="True">Compatible Hits</option>
+                    <option value="--total-hits-norm">All Hits</option>
                 </param>
                 <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus"
                     help="Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 500,000" />
@@ -398,7 +398,5 @@
   --num-frag-assign-draws        For each fragment drawn from a transcript, Cuffdiff will assign it this many times (probabilistically), thus estimating the assignment uncertainty for each transcript. Used to estimate the variance-covariance matrix on assigned fragment counts.
   --min-reps-for-js-test         Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates.
     </help>
-    <citations>
-        <citation type="doi">10.1038/nbt.1621</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>
diff -r d3ae7d9c2202 -r 43b36b3d4333 cummeRbund.R
--- a/cummeRbund.R	Sun Feb 19 12:12:17 2017 -0500
+++ b/cummeRbund.R	Tue Jun 16 13:00:02 2020 -0400
@@ -1,2 +1,2 @@
 library("cummeRbund")
-cuff <- readCufflinks(dir = ".", dbFile = 'cummeRbund.sqlite')
\ No newline at end of file
+cuff <- readCufflinks(dir = ".", dbFile = "cummeRbund.sqlite")