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comparison htseq-count.xml @ 8:5bfb7a651fac

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author lparsons
date Fri, 21 Sep 2012 17:57:47 -0400
parents 8a5d43b21c6e
children 971e20519fb8
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5:8a5d43b21c6e 8:5bfb7a651fac
1 <tool id="htseq_count" name="htseq-count" version="0.2"> 1 <tool id="htseq_count" name="htseq-count" version="0.2.1">
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="1.6.2">numpy</requirement> 5 <requirement type="package" version="1.6.2">numpy</requirement>
6 <requirement type="package" version="0.5.3p9">htseq</requirement> 6 <requirement type="package" version="0.5.3p9">htseq</requirement>
23 #end if 23 #end if
24 htseq-count 24 htseq-count
25 --mode=$mode 25 --mode=$mode
26 --stranded=$stranded 26 --stranded=$stranded
27 --minaqual=$minaqual 27 --minaqual=$minaqual
28 --type=$type 28 --type=$featuretype
29 --idattr=$idattr 29 --idattr=$idattr
30 #if $samout_conditional.samout: 30 #if $samout_conditional.samout:
31 --samout=$__new_file_path__/${samoutfile.id}_tmp 31 --samout=$__new_file_path__/${samoutfile.id}_tmp
32 #end if 32 #end if
33 #if $samfile.extension == "bam": 33 #if $samfile.extension == "bam":
40 #if $samout_conditional.samout: 40 #if $samout_conditional.samout:
41 &amp;&amp; samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile 41 &amp;&amp; samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile
42 #end if</command> 42 #end if</command>
43 <inputs> 43 <inputs>
44 <param format="sam, bam" name="samfile" type="data" label="Aligned SAM/BAM File"> 44 <param format="sam, bam" name="samfile" type="data" label="Aligned SAM/BAM File">
45 <help>Paired-End data MUST be sorted by QUERY NAME, use Picard Read Mate Fixer and Query name sort order before using this tool on paired data</help> 45 <help>Paired-End data MUST be sorted by QUERY NAME, use "NGS: Picard - Paired Read Mate Fixer" to sort by QUERY NAME and output to SAM (not BAM) before using this tool on paired data.</help>
46 </param> 46 </param>
47 <param format="gff" name="gfffile" type="data" label="GFF File"/> 47 <param format="gff" name="gfffile" type="data" label="GFF File"/>
48 <param name="mode" type="select" label="Mode"> 48 <param name="mode" type="select" label="Mode">
49 <help>Mode to handle reads overlapping more than one feature.</help> 49 <help>Mode to handle reads overlapping more than one feature.</help>
50 <option value="union" selected="true">Union</option> 50 <option value="union" selected="true">Union</option>
58 <option value="reverse">Reverse</option> 58 <option value="reverse">Reverse</option>
59 </param> 59 </param>
60 <param name="minaqual" type="integer" value="0" label="Minimum alignment quality"> 60 <param name="minaqual" type="integer" value="0" label="Minimum alignment quality">
61 <help>Skip all reads with alignment quality lower than the given minimum value</help> 61 <help>Skip all reads with alignment quality lower than the given minimum value</help>
62 </param> 62 </param>
63 <param name="type" type="text" value="exon" label="Feature type"> 63 <param name="featuretype" type="text" value="exon" label="Feature type">
64 <help>Feature type (3rd column in GFF file) to be used. All features of other types are ignored. The default, suitable for RNA-Seq and Ensembl GTF files, is exon.</help> 64 <help>Feature type (3rd column in GFF file) to be used. All features of other types are ignored. The default, suitable for RNA-Seq and Ensembl GTF files, is exon.</help>
65 </param> 65 </param>
66 <param name="idattr" type="text" value="gene_id" label="ID Attribute"> 66 <param name="idattr" type="text" value="gene_id" label="ID Attribute">
67 <help>GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. All features of the specified type MUST have a value for this attribute. The default, suitable for RNA-SEq and Ensembl GTF files, is gene_id.</help> 67 <help>GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. All features of the specified type MUST have a value for this attribute. The default, suitable for RNA-SEq and Ensembl GTF files, is gene_id.</help>
68 </param> 68 </param>
104 <exit_code range="1:" level="fatal" description="Unknown error occurred" /> 104 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
105 <regex match="htseq-count: command not found" source="stderr" level="fatal" description="The HTSeq python package is not properly installed, contact Galaxy administrators" /> 105 <regex match="htseq-count: command not found" source="stderr" level="fatal" description="The HTSeq python package is not properly installed, contact Galaxy administrators" />
106 <regex match="samtools: command not found" source="stderr" level="fatal" description="The samtools package is not properly installed, contact Galaxy administrators" /> 106 <regex match="samtools: command not found" source="stderr" level="fatal" description="The samtools package is not properly installed, contact Galaxy administrators" />
107 <regex match="Error: Feature (.+) does not contain a '(.+)' attribute" source="both" level="fatal" description="Error parsing the GFF file, at least one feature of the specified 'Feature type' does not have a value for the specified 'ID Attribute'" /> 107 <regex match="Error: Feature (.+) does not contain a '(.+)' attribute" source="both" level="fatal" description="Error parsing the GFF file, at least one feature of the specified 'Feature type' does not have a value for the specified 'ID Attribute'" />
108 <regex match="Error occured in line (\d+) of file" source="stderr" level="fatal" description="Unknown error parsing the GFF file" /> 108 <regex match="Error occured in line (\d+) of file" source="stderr" level="fatal" description="Unknown error parsing the GFF file" />
109 <regex match="Error" source="stderr" level="fatal" description="Unknown error occured" />
109 </stdio> 110 </stdio>
110 111
111 <tests> 112 <tests>
112 <test> 113 <test>
113 <param name="samfile" value="htseq-test.sam" /> 114 <param name="samfile" value="htseq-test.sam" />