# HG changeset patch
# User devteam
# Date 1486510864 18000
# Node ID 9f243677c4c67149253664487e6046fca7f77185
# Parent  12aeae6d858713ba7cdc537b32d57efc6a930f2e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f

diff -r 12aeae6d8587 -r 9f243677c4c6 cuff_macros.xml
--- a/cuff_macros.xml	Tue Jun 07 17:58:15 2016 -0400
+++ b/cuff_macros.xml	Tue Feb 07 18:41:04 2017 -0500
@@ -28,21 +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>
@@ -50,16 +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>
@@ -81,11 +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 12aeae6d8587 -r 9f243677c4c6 gffread.xml
--- a/gffread.xml	Tue Jun 07 17:58:15 2016 -0400
+++ b/gffread.xml	Tue Feb 07 18:41:04 2017 -0500
@@ -1,7 +1,5 @@
 <tool id="gffread" name="gffread" version="@VERSION@.0">
     <description>Filters and/or converts GFF3/GTF2 records</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
     <macros>
         <import>cuff_macros.xml</import>
         <xml name="fasta_output_select">
@@ -49,14 +47,16 @@
             </param>
         </xml>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <command>
 <![CDATA[
     #if $reference_genome.source == 'history':
-        ln -s $reference_genome.genome_fasta genomeref.fa &&
+        ln -s '$reference_genome.genome_fasta' genomeref.fa &&
     #end if
-    gffread $input
+    gffread '$input'
     #if $reference_genome.source == 'cached':
-        -g "${reference_genome.fasta_indexes.fields.path}"
+        -g '${reference_genome.fasta_indexes.fields.path}'
         #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
             #echo ' '.join(str($reference_genome.ref_filtering).split(','))
         #end if
@@ -74,7 +74,7 @@
         -i $maxintron
     #end if
     #if $region.region_filter == 'filter':
-        -r $region.range $region.discard_partial
+        -r '$region.range' $region.discard_partial
     #end if
     #if $merging.merge_sel != 'none':
         $merging.merge_cmd
@@ -83,7 +83,7 @@
         #end if
     #end if
     #if $chr_replace:
-        -m "$chr_replace"
+        -m '$chr_replace'
     #end if
     ##
     ## Although documented, does not appear to be used in the gffread code
@@ -99,7 +99,7 @@
     #end if
     #if $gffs.gff_fmt != 'none':
         #if $gffs.tname:
-            -t "$gffs.tname"
+            -t '$gffs.tname'
         #end if
         #if $gffs.gff_fmt == 'gff':
             #if $input.datatype.file_ext == 'gft':
@@ -141,8 +141,8 @@
                     </help>
                     <validator type="regex">(([+-])?(\w+:))?\d+\.\.\d+</validator>
                 </param>
-                <param name="discard_partial" type="boolean" truevalue="-R" falsevalue="" check="false"
-                       label="discard all transcripts that are not fully contained within the given range" help="(-R)"/>
+                <param name="discard_partial" type="boolean" truevalue="-R" falsevalue="" checked="false"
+                       label="Discard all transcripts that are not fully contained within the given range" help="(-R)"/>
             </when>
         </conditional>
         <param name="maxintron" type="integer" value="" optional="true" min="0" label="Filter out transcipts with large introns"
@@ -218,7 +218,7 @@
             </when>
             <when value="gff">
                 <param name="output_cmd" type="hidden" value="-o output.gff3"/>
-                <param name="ensembl" type="boolean" truevalue="-L" falsevalue="" check="false" label="Ensembl GTF to GFF3 conversion" help="(-L)"/>
+                <param name="ensembl" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Ensembl GTF to GFF3 conversion" help="(-L)"/>
                 <expand macro="trackname" />
             </when>
             <when value="gtf">
@@ -227,11 +227,11 @@
             </when>
         </conditional>
 
-        <param name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" check="false"
+        <param name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" checked="false"
                        label="full GFF attribute preservation (all attributes are shown)" help="(-F)"/>
-        <param name="decode_url" type="boolean" truevalue="-D" falsevalue="" check="false"
+        <param name="decode_url" type="boolean" truevalue="-D" falsevalue="" checked="false"
                        label="decode url encoded characters within attributes" help="(-D)"/>
-        <param name="expose" type="boolean" truevalue="-E" falsevalue="" check="false"
+        <param name="expose" type="boolean" truevalue="-E" falsevalue="" checked="false"
                        label="warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records" help="(-E)"/>
 
     </inputs>
@@ -259,7 +259,7 @@
         <test>
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
             <param name="gff_fmt" value="gff"/>
-            <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" />
+            <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" />
         </test>
 
         <test>
@@ -269,7 +269,7 @@
             <output name="output_gtf">
                 <assert_contents>
                     <not_has_text text="pseudo" />
-		</assert_contents>
+                </assert_contents>
             </output>
         </test>
 
@@ -282,7 +282,7 @@
                 <assert_contents>
                     <has_text text="ENST00000587541" />
                     <has_text text="ENST00000382683" />
-		</assert_contents>
+                </assert_contents>
             </output>
         </test>
 
@@ -294,9 +294,9 @@
             <param name="gff_fmt" value="gtf"/>
             <output name="output_gtf">
                 <assert_contents>
-                    <has_text text="ENST00000587541" />
+                    <not_has_text text="ENST00000587541" />
                     <has_text text="ENST00000382683" />
-		</assert_contents>
+                </assert_contents>
             </output>
         </test>
 
@@ -310,7 +310,7 @@
                 <assert_contents>
                     <not_has_text text="ENST00000587541" />
                     <has_text text="ENST00000382683" />
-		</assert_contents>
+                </assert_contents>
             </output>
         </test>
 
@@ -318,7 +318,7 @@
             <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
             <param name="source" value="history"/>
             <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/>
-            <param name="fa_outputs" value="-w exons.f,-x cds.fa,-y pep.fa"/>
+            <param name="fa_outputs" value="-w exons.fa,-x cds.fa,-y pep.fa"/>
             <param name="region_filter" value="filter"/>
             <param name="range" value="19:496500..504965"/>
             <param name="gff_fmt" value="gtf"/>
@@ -326,25 +326,25 @@
                 <assert_contents>
                     <not_has_text text="ENST00000587541" />
                     <has_text text="ENST00000382683" />
-		</assert_contents>
+                </assert_contents>
             </output>
             <output name="output_exons">
                 <assert_contents>
                     <has_text text="ENST00000346144 gene=MADCAM1 CDS=47-932" />
                     <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" />
-		</assert_contents>
+                </assert_contents>
             </output>
             <output name="output_cds">
                 <assert_contents>
                     <has_text text="ENST00000346144 gene=MADCAM1" />
                     <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" />
-		</assert_contents>
+                </assert_contents>
             </output>
             <output name="output_pep">
                 <assert_contents>
                     <has_text text="ENST00000346144 gene=MADCAM1" />
                     <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" />
-		</assert_contents>
+                </assert_contents>
             </output>
         </test>