Mercurial > repos > lparsons > htseq_count
comparison htseq-count.xml @ 3:f7a5b54a8d4f
Split feature and non-feature counts, removed tool_dependencies.xml (for now)
author | Lance Parsons <lparsons@princeton.edu> |
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date | Mon, 10 Sep 2012 17:30:10 -0400 |
parents | 3fdeebd7e710 |
children | 14bec14f4290 |
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2:f5d08224af89 | 3:f7a5b54a8d4f |
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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 > $counts | 38 | 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 |
39 #if $samout_conditional.samout: | 39 #if $samout_conditional.samout: |
40 && samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile | 40 && 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 |