# HG changeset patch
# User iuc
# Date 1474469981 14400
# Node ID 6e5c95760ab15afb48b543f4aa4ad11de66cd291
# Parent  55ed198f2c1c9d2348543c34ae162b0f618c626f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790

diff -r 55ed198f2c1c -r 6e5c95760ab1 htseq-count.xml
--- a/htseq-count.xml	Tue Sep 20 17:51:06 2016 -0400
+++ b/htseq-count.xml	Wed Sep 21 10:59:41 2016 -0400
@@ -28,6 +28,7 @@
             #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path )
         #end if
     #end if
+    
     #if $force_sort == "True":
         #if $samfile.extension == 'bam':
             samtools sort -n "$samfile" "name_sorted_alignment" &&
@@ -35,14 +36,15 @@
             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="$idattr"
+        --mode=$mode
+        --stranded=$stranded
+        --minaqual=$minaqual
+        --type="$featuretype"
+        --idattr="$idattr"
     #if $samout_conditional.samout == "Yes":
-        --samout=$__new_file_path__/${samoutfile.id}_tmp
+        --samout='$__new_file_path__/${samoutfile.id}_tmp'
     #end if
     #if $force_sort == "True":
         --order=name
@@ -51,12 +53,18 @@
     #else
         --order=pos
         --format=$samfile.extension
-        $samfile
+        '$samfile'
     #end if
-    "$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
+    
+    "$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 $samout_conditional.samout == "Yes":
-        && samtools view -Su -t "${reference_fasta_filename}.fai" "$__new_file_path__/${samoutfile.id}_tmp" | samtools sort -o - sorted > "$samoutfile"
+        && samtools view -Su
+            -t "${reference_fasta_filename}.fai"
+            "$__new_file_path__/${samoutfile.id}_tmp"
+        | samtools sort -o - name_sorted_alignment > "$samoutfile"
     #end if
     ]]>
     </command>
@@ -105,7 +113,7 @@
                             <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                         </param>
                     </when>
-                    <when value="history"> <!-- FIX ME!!!! -->
+                    <when value="history">
                         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
                     </when>
                 </conditional>
@@ -120,7 +128,11 @@
     </inputs>
 
     <outputs>
-        <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}"/>
+        <data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}">
+            <actions>
+                <action name="column_names" type="metadata" default="Geneid,${samfile.name}" />
+            </actions>
+        </data>
         <data format="tabular" name="othercounts" metadata_source="samfile" label="${tool.name} on ${on_string} (no feature)"/>
         <data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)">
             <filter>samout_conditional['samout'] == "Yes"</filter>
@@ -167,19 +179,17 @@
             <output name="counts" file="htseq-test-paired_counts.tsv" />
             <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />
         </test>
-
-        <!-- Seems to be an issue setting the $reference_fasta_filename variable during test
+        
         <test>
             <param name="samfile" value="htseq-test.sam" />
             <param name="gfffile" value="htseq-test.gff" />
-            <param name="samout" value="True" />
+            <param name="samout" value="Yes" />
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" value="htseq-test_reference.fasta" />
             <output name="counts" file="htseq-test_counts.tsv" />
             <output name="othercounts" file="htseq-test_othercounts.tsv" />
             <output name="samoutfile" file="htseq-test_samout.bam" />
         </test>
-        -->
     </tests>
 
     <help>
@@ -277,28 +287,6 @@
     </help>
 
     <citations>
-        <citation type="bibtex">
-@article{anders_htseqpython_2015,
-    title = {{HTSeq}—a {Python} framework to work with high-throughput sequencing data},
-    volume = {31},
-    issn = {1367-4803, 1460-2059},
-    url = {http://bioinformatics.oxfordjournals.org/content/31/2/166},
-    doi = {10.1093/bioinformatics/btu638},
-    abstract = {Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed.
-Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.
-Availability and implementation: HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq.
-Contact: sanders\{at\}fs.tum.de},
-    language = {en},
-    number = {2},
-    urldate = {2015-04-21},
-    journal = {Bioinformatics},
-    author = {Anders, Simon and Pyl, Paul Theodor and Huber, Wolfgang},
-    month = jan,
-    year = {2015},
-    pmid = {25260700},
-    pages = {166--169},
-    }
-}
-        </citation>
+        <citation type="doi">10.1093/bioinformatics/btu638</citation>
     </citations>
 </tool>
diff -r 55ed198f2c1c -r 6e5c95760ab1 test-data/htseq-test_reference.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/htseq-test_reference.fasta	Wed Sep 21 10:59:41 2016 -0400
@@ -0,0 +1,36 @@
+>2-micron
+actg
+>MT
+actg
+>I
+actg
+>VI
+actg
+>III
+actg
+>IX
+actg
+>VIII
+actg
+>V
+actg
+>XI
+actg
+>X
+actg
+>XIV
+actg
+>II
+actg
+>XIII
+actg
+>XVI
+actg
+>XII
+actg
+>VII
+actg
+>XV
+actg
+>IV
+actg
diff -r 55ed198f2c1c -r 6e5c95760ab1 test-data/htseq-test_samout.bam
Binary file test-data/htseq-test_samout.bam has changed