# HG changeset patch
# User devteam
# Date 1486510791 18000
# Node ID 96c4d0e185462f929c35a3fe4d21a77fdc11ce2b
# Parent  baeea9c2ff0fd56c2ce00b0b76ddf2210066dc69
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f

diff -r baeea9c2ff0f -r 96c4d0e18546 cuff_macros.xml
--- a/cuff_macros.xml	Mon Nov 09 12:06:36 2015 -0500
+++ b/cuff_macros.xml	Tue Feb 07 18:39:51 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 baeea9c2ff0f -r 96c4d0e18546 gffread.xml
--- a/gffread.xml	Mon Nov 09 12:06:36 2015 -0500
+++ b/gffread.xml	Tue Feb 07 18:39:51 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">
@@ -18,7 +16,7 @@
                 <option value="-J">discard any mRNAs that either lack initial START codon or the terminal STOP codon, or have an in-frame stop codon (-J)</option>
                 <option value="-V">discard any mRNAs with CDS having in-frame stop codons (-V)</option>
                 <option value="-H">check and adjust the starting CDS phase if the original phase leads to a translation with an in-frame stop codon (-H with -V)</option>
-                <!-- gffread bug: B not in  missing from param to the arg parser 
+                <!-- gffread bug: B not in  missing from param to the arg parser
                 <option value="-B">single-exon transcripts are also checked on the opposite strand (-B with -V)</option>
                 -->
             </param>
@@ -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':
@@ -121,7 +121,7 @@
             <option value="-G">only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input) (-G)</option>
             <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option>
             <option value="--no-pseudo">filter out records matching the 'pseudo' keyword (--no-pseudo)</option>
-        </param> 
+        </param>
         <conditional name="region">
             <param name="region_filter" type="select" label="Filter by genome region">
                 <option value="none">No</option>
@@ -131,21 +131,21 @@
             <when value="filter">
                 <param name="range" type="text" value="" label="Only show transcripts overlapping coordinate range">
                     <help><![CDATA[
-                    (-r [['strand']'chr':]'start'..'end') <br> 
-                    examples: <br> 
-                    1000..500000 <br> 
-                    chr1:1000..500000 <br> 
-                    +chr1:1000..500000 <br> 
+                    (-r [['strand']'chr':]'start'..'end') <br>
+                    examples: <br>
+                    1000..500000 <br>
+                    chr1:1000..500000 <br>
+                    +chr1:1000..500000 <br>
                     -chr1:1000..500000
                     ]]>
                     </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" 
+        <param name="maxintron" type="integer" value="" optional="true" min="0" label="Filter out transcipts with large introns"
                help="If set, discard transcripts having an intron larger (-i max_intron)"/>
         <param name="chr_replace" type="data" format="tabular" optional="true" label="Replace reference sequence names" >
             <help><![CDATA[(-m chr_replace) <br>
@@ -154,7 +154,7 @@
                 NOTE: GFF records on reference sequences that are not found among the "original_ref_ID" entries in this file will be filtered out
                 ]]>
             </help>
-        </param> 
+        </param>
 
         <!-- Although documented, does not appear to be used in the gffread code
         <param name="seq_info" type="data" format="tabular" optional="true" label="Use the description field as the value for a 'descr' attribute to the GFF record">
@@ -163,7 +163,7 @@
                   seq_info input file is a 3 column tab-delimited file providing this info for each of the mapped sequences: &lt;br&gt;
                   "seq-name" "seq-length" "seq-description" &lt;br&gt;
             </help>
-        </param> 
+        </param>
         -->
 
         <!-- merging -->
@@ -201,7 +201,7 @@
                 <expand macro="fasta_output_select" />
             </when>
             <when value="history">
-                <param name="genome_fasta" type="data" format="fasta" label="Genome Reference Fasta"/> 
+                <param name="genome_fasta" type="data" format="fasta" label="Genome Reference Fasta"/>
                 <expand macro="ref_filtering_select" />
                 <expand macro="fasta_output_select" />
             </when>
@@ -209,7 +209,7 @@
 
         <!-- outputs -->
         <conditional name="gffs">
-            <param name="gff_fmt" type="select" optional="true" label="Feature File Output" help="(-o output.gff3|output.gtf)">
+            <param name="gff_fmt" type="select" label="Feature File Output" help="(-o output.gff3|output.gtf)">
                 <option value="none">none</option>
                 <option value="gff">GFF</option>
                 <option value="gtf">GTF</option>
@@ -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>
 
@@ -359,11 +359,11 @@
 
 Usage: ::
 
- gffread "input_gff" [-g "genomic_seqs_fasta" | "dir"][-s "seq_info.fsize"] 
+ gffread "input_gff" [-g "genomic_seqs_fasta" | "dir"][-s "seq_info.fsize"]
    [-o "outfile.gff"] [-t "tname"] [-r [["strand"]"chr":]"start".."end" [-R]]
    [-CTVNJMKQAFGUBHZWTOLE] [-w "exons.fa"] [-x "cds.fa"] [-y "tr_cds.fa"]
-   [-i "maxintron"] 
- 
+   [-i "maxintron"]
+
 Options: ::
 
   -g  full path to a multi-fasta file with the genomic sequences
@@ -376,7 +376,7 @@
   -i  discard transcripts having an intron larger than <maxintron>
   -r  only show transcripts overlapping coordinate range <start>..<end>
       (on chromosome/contig <chr>, strand <strand> if provided)
-  -R  for -r option, discard all transcripts that are not fully 
+  -R  for -r option, discard all transcripts that are not fully
       contained within the given range
   -U  discard single-exon transcripts
   -C  coding only: discard mRNAs that have no CDS feature
@@ -385,12 +385,12 @@
       and move them to the mRNA level (useful for GTF input)
   -A  use the description field from <seq_info.fsize> and add it
       as the value for a 'descr' attribute to the GFF record
-  
+
   -O  process also non-transcript GFF records (by default non-transcript
       records are ignored)
   -V  discard any mRNAs with CDS having in-frame stop codons
   -H  for -V option, check and adjust the starting CDS phase
-      if the original phase leads to a translation with an 
+      if the original phase leads to a translation with an
       in-frame stop codon
   -B  for -V option, single-exon transcripts are also checked on the
       opposite strand
@@ -400,7 +400,7 @@
       or the terminal STOP codon, or have an in-frame stop codon
       (only print mRNAs with a fulll, valid CDS)
   --no-pseudo: filter out records matching the 'pseudo' keyword
- 
+
   -M/--merge : cluster the input transcripts into loci, collapsing matching
        transcripts (those with the same exact introns and fully contained)
   -d <dupinfo> : for -M option, write collapsing info to file <dupinfo>
@@ -410,10 +410,10 @@
   -Q  for -M option, remove the containment restriction:
       (multi-exon transcripts will be collapsed if just their introns match,
       while single-exon transcripts can partially overlap (80%))
- 
-  --force-exons: make sure that the lowest level GFF features are printed as 
+
+  --force-exons: make sure that the lowest level GFF features are printed as
       "exon" features
-  -E  expose (warn about) duplicate transcript IDs and other potential 
+  -E  expose (warn about) duplicate transcript IDs and other potential
       problems with the given GFF/GTF records
   -D  decode url encoded characters within attributes
   -Z  merge close exons into a single exon (for intron size<4)
diff -r baeea9c2ff0f -r 96c4d0e18546 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 09 12:06:36 2015 -0500
+++ b/tool_dependencies.xml	Tue Feb 07 18:39:51 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>