htseq_count: htseq-count.xml comparison

comparison htseq-count.xml @ 23:6e5c95760ab1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit ee302cfd1ae3f7fcb3def4359e372341a7272790

author	iuc
date	Wed, 21 Sep 2016 10:59:41 -0400
parents	55ed198f2c1c
children	620d5603d1a8

comparison

equal deleted inserted replaced

-:55ed198f2c1c
+:6e5c95760ab1
 samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 &&
 #else:
 #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" &&
 #else
 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"
 #if $samout_conditional.samout == "Yes":
---samout=$__new_file_path__/${samoutfile.id}_tmp
+--samout='$__new_file_path__/${samoutfile.id}_tmp'
 #end if
 #if $force_sort == "True":
 --order=name
 --format=bam
 name_sorted_alignment.bam
 #else
 --order=pos
 --format=$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 > "$samoutfile"
 #end if
 ]]>
 </command>
 <inputs>
 <filter type="data_meta" key="dbkey" ref="samfile" column="1"/>
 </options>
 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
 </param>
 </when>
-<when value="history"> <!-- FIX ME!!!! -->
+<when value="history">
 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
 </when>
 </conditional>
 </when>
 <when value="No">
 <help>This option can be used for for paired-end data that has many unmapped mates. Use this if you get the warning about paired end data missing or not being properly sorted.</help>
 </param>
 </inputs>
 <outputs>
-<data format="tabular" name="counts" metadata_source="samfile" label="${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>
 </data>
 </outputs>
 <param name="samout" value="No" />
 <param name="force_sort" value="True" />
 <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>
 <![CDATA[
 Overview
 Public License v3. Part of the 'HTSeq' framework.
 ]]>
 </help>
 <citations>
-<citation type="bibtex">
+<citation type="doi">10.1093/bioinformatics/btu638</citation>
-@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>
 </citations>
 </tool>

Mercurial > repos > lparsons > htseq_count

comparison htseq-count.xml @ 23:6e5c95760ab1 draft