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comparison htseq-count.xml @ 3:f7a5b54a8d4f

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Split feature and non-feature counts, removed tool_dependencies.xml (for now)
author Lance Parsons <lparsons@princeton.edu>
date Mon, 10 Sep 2012 17:30:10 -0400
parents 3fdeebd7e710
children 14bec14f4290
comparison
equal deleted inserted replaced
2:f5d08224af89 3:f7a5b54a8d4f
1 <tool id="htseq_count" name="htseq-count" version="0.1"> 1 <tool id="htseq_count" name="htseq-count" version="0.2">
2 <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description> 2 <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
3 <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command> 3 <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.5.3p9">htseq</requirement> 5 <requirement type="package" version="0.5.3p9">htseq</requirement>
6 <requirement type="package" version="0.1.18">samtools</requirement> 6 <requirement type="package" version="0.1.18">samtools</requirement>
33 - 33 -
34 #else 34 #else
35 $samfile 35 $samfile
36 #end if 36 #end if
37 $gfffile 37 $gfffile
38 &gt; $counts 38 | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&amp;2"; else print $0}' &gt; $counts 2&gt;$othercounts
39 #if $samout_conditional.samout: 39 #if $samout_conditional.samout:
40 &amp;&amp; samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile 40 &amp;&amp; samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile
41 #end if</command> 41 #end if</command>
42 <inputs> 42 <inputs>
43 <param format="sam, bam" name="samfile" type="data" label="Aligned SAM File"> 43 <param format="sam, bam" name="samfile" type="data" label="Aligned SAM File">
91 </conditional> 91 </conditional>
92 </inputs> 92 </inputs>
93 93
94 <outputs> 94 <outputs>
95 <data format="tabular" name="counts" label="${tool.name} on ${on_string}"/> 95 <data format="tabular" name="counts" label="${tool.name} on ${on_string}"/>
96 <data format="tabular" name="othercounts" label="${tool.name} on ${on_string} (no feature)"/>
96 <data format="bam" name="samoutfile" label="${tool.name} on ${on_string} (BAM)"> 97 <data format="bam" name="samoutfile" label="${tool.name} on ${on_string} (BAM)">
97 <filter>samout_conditional['samout']</filter> 98 <filter>samout_conditional['samout']</filter>
98 </data> 99 </data>
99 </outputs> 100 </outputs>
100 101
106 <test> 107 <test>
107 <param name="samfile" value="htseq-test.sam" /> 108 <param name="samfile" value="htseq-test.sam" />
108 <param name="gfffile" value="htseq-test.gff" /> 109 <param name="gfffile" value="htseq-test.gff" />
109 <param name="samout" value="False" /> 110 <param name="samout" value="False" />
110 <output name="counts" file="htseq-test_counts.tsv" /> 111 <output name="counts" file="htseq-test_counts.tsv" />
112 <output name="othercounts" file="htseq-test_othercounts.tsv" />
111 </test> 113 </test>
112 <test> 114 <test>
113 <param name="samfile" value="htseq-test.bam" /> 115 <param name="samfile" value="htseq-test.bam" />
114 <param name="gfffile" value="htseq-test.gff" /> 116 <param name="gfffile" value="htseq-test.gff" />
115 <param name="samout" value="False" /> 117 <param name="samout" value="False" />
116 <output name="counts" file="htseq-test_counts.tsv" /> 118 <output name="counts" file="htseq-test_counts.tsv" />
119 <output name="othercounts" file="htseq-test_othercounts.tsv" />
117 </test> 120 </test>
118 <!-- Seems to be an issue setting the $reference_fasta_filename variable during test 121 <!-- Seems to be an issue setting the $reference_fasta_filename variable during test
119 <test> 122 <test>
120 <param name="samfile" value="htseq-test.sam" /> 123 <param name="samfile" value="htseq-test.sam" />
121 <param name="gfffile" value="htseq-test.gff" /> 124 <param name="gfffile" value="htseq-test.gff" />
122 <param name="samout" value="True" /> 125 <param name="samout" value="True" />
123 <param name="reference_source_selector" value="history" /> 126 <param name="reference_source_selector" value="history" />
124 <param name="ref_file" value="htseq-test_reference.fasta" /> 127 <param name="ref_file" value="htseq-test_reference.fasta" />
125 <output name="counts" file="htseq-test_counts.tsv" /> 128 <output name="counts" file="htseq-test_counts.tsv" />
129 <output name="othercounts" file="htseq-test_othercounts.tsv" />
126 <output name="samoutfile" file="htseq-test_samout.bam" /> 130 <output name="samoutfile" file="htseq-test_samout.bam" />
127 </test> 131 </test>
128 --> 132 -->
129 </tests> 133 </tests>
130 134