Mercurial > repos > lparsons > htseq_count
diff htseq-count.xml @ 16:227f9d3f0e32 draft
Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions
| author | lparsons |
|---|---|
| date | Fri, 11 Apr 2014 15:05:28 -0400 |
| parents | 3ffe4e2572a7 |
| children | d5edaf8dc974 |
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--- a/htseq-count.xml Mon Jan 27 14:12:46 2014 -0500 +++ b/htseq-count.xml Fri Apr 11 15:05:28 2014 -0400 @@ -1,11 +1,10 @@ -<tool id="htseq_count" name="htseq-count" version="0.3.2"> +<tool id="htseq_count" name="htseq-count" version="0.4"> <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description> <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command> <requirements> <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="0.5.4p5">htseq</requirement> + <requirement type="package" version="0.6.1">htseq</requirement> <requirement type="package" version="0.1.19">samtools</requirement> - <requirement type="package" version="1.56.0">picard</requirement> </requirements> <command> ##set up input files @@ -18,18 +17,9 @@ #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path ) #end if #end if - #if str($singlepaired) == "paired": - ln -s $samfile local_input.sam && - java -Xmx2G -jar "\$JAVA_JAR_PATH/SortSam.jar" VALIDATION_STRINGENCY=LENIENT SORT_ORDER=queryname O=prepared_input.sam I=local_input.sam TMP_DIR="${__new_file_path__}" - || echo "Error running Picard MergeSamFiles" >&2 && - #else: - #if $samfile.extension == "bam": - samtools view $samfile | - #else - ln -s $samfile prepared_input.sam && - #end if - #end if htseq-count + --format=$samfile.extension + --order=pos --mode=$mode --stranded=$stranded --minaqual=$minaqual @@ -38,27 +28,14 @@ #if $samout_conditional.samout: --samout=$__new_file_path__/${samoutfile.id}_tmp #end if - #if str($singlepaired) == "paired": - prepared_input.sam - #else: - #if $samfile.extension == "bam": - - - #else: - prepared_input.sam - #end if - #end if + $samfile $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 #end if</command> <inputs> - <param format="sam, bam" name="samfile" type="data" label="Aligned SAM/BAM File"/> - <param name="singlepaired" type="select" label="Is this library mate-paired?"> - <help>Paired libraries will be sorted by read name prior to counting.</help> - <option value="single" selected="true">single-end</option> - <option value="paired">paired-end</option> - </param> + <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"> <help>Mode to handle reads overlapping more than one feature.</help> @@ -72,7 +49,7 @@ <option value="no">No</option> <option value="reverse">Reverse</option> </param> - <param name="minaqual" type="integer" value="0" label="Minimum alignment quality"> + <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> </param> <param name="featuretype" type="text" value="exon" label="Feature type"> @@ -188,8 +165,7 @@ The following figure illustrates the effect of these three modes: -.. image:: $PATH_TO_IMAGES/count_modes.png - :width: 500 +.. image:: count_modes.png Strandedness