# HG changeset patch
# User lparsons
# Date 1435006623 14400
# Node ID 19e80c732870737c4004f105357eb8a5a79badd7
# Parent  6b61ba6dd9e274d0efed563f03e4fc8af6daea9b
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/htseq_count commit 8a40cf16ce0b48cdfda88a505869e77e8826cb23

diff -r 6b61ba6dd9e2 -r 19e80c732870 htseq-count.xml
--- a/htseq-count.xml	Mon Jun 22 14:18:42 2015 -0400
+++ b/htseq-count.xml	Mon Jun 22 16:57:03 2015 -0400
@@ -31,17 +31,17 @@
     #end if
     #if $force_sort:
         #if $samfile.extension == 'bam':
-            samtools sort -n $samfile "name_sorted_alignment" &&
+            samtools sort -n "$samfile" "name_sorted_alignment" &&
         #else
-            samtools view -Su -t ${reference_fasta_filename}.fai $samfile | samtools sort -n - "name_sorted_alignment" &&
+            samtools view -Su -t ${reference_fasta_filename}.fai "$samfile" | samtools sort -n - "name_sorted_alignment" &&
         #end if
     #end if
     htseq-count
     --mode=$mode
     --stranded=$stranded
     --minaqual=$minaqual
-    --type=$featuretype
-    --idattr=$idattr
+    --type="$featuretype"
+    --idattr="$idattr"
     #if $samout_conditional.samout:
         --samout=$__new_file_path__/${samoutfile.id}_tmp
     #end if
@@ -54,7 +54,7 @@
         --format=$samfile.extension
         $samfile
     #end if
-    $gfffile
+    "$gfffile"
     | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&2"; else print $0}' > $counts 2>$othercounts
     #if $samout_conditional.samout:
         && samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile
@@ -65,23 +65,23 @@
     <inputs>
         <param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>
         <param format="gff" name="gfffile" type="data" label="GFF File"/>
-        <param name="mode" type="select" label="Mode">
+        <param name="mode" type="select" label="Mode" help="(--mode)">
             <help>Mode to handle reads overlapping more than one feature.</help>
             <option value="union" selected="true">Union</option>
             <option value="intersection-strict">Intersection (strict)</option>
             <option value="intersection-nonempty">Intersection (nonempty)</option>
         </param>
-        <param name="stranded" type="select" label="Stranded">
+        <param name="stranded" type="select" label="Stranded" help="(--stranded)">
             <help>Specify whether the data is from a strand-specific assay. 'Reverse' means yes with reversed strand interpretation.</help>
             <option value="yes" selected="true">Yes</option>
             <option value="no">No</option>
             <option value="reverse">Reverse</option>
         </param>
         <param name="minaqual" type="integer" value="10" label="Minimum alignment quality">
-            <help>Skip all reads with alignment quality lower than the given minimum value</help>
+            <help>Skip all reads with alignment quality lower than the given minimum value. (-minaqual)</help>
         </param>
         <param name="featuretype" type="text" value="exon" label="Feature type">
-            <help>Feature type (3rd column in GFF file) to be used. All features of other types are ignored. The default, suitable for RNA-Seq and Ensembl GTF files, is exon.</help>
+            <help>Feature type (3rd column in GFF file) to be used. All features of other types are ignored. The default, suitable for RNA-Seq and Ensembl GTF files, is exon. (--type)</help>
         </param>
         <param name="idattr" type="text" value="gene_id" label="ID Attribute">
             <help>GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. All features of the specified type MUST have a value for this attribute. The default, suitable for RNA-Seq and Ensembl GTF files, is gene_id.</help>