Mercurial > repos > greg > affy2vcf
comparison affy2vcf.xml @ 2:02025c366fca draft
Uploaded
author | greg |
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date | Thu, 01 Nov 2018 09:11:57 -0400 |
parents | a2f0931898be |
children | 6274184a8b84 |
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1:a2f0931898be | 2:02025c366fca |
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1 <tool id="affr2vcf" name="Convert Affymetrix" version="1.9"> | 1 <tool id="affr2vcf" name="Convert Affymetrix" version="@WRAPPER_VERSION@"> |
2 <description>genotype calls and intensities to VCF</description> | 2 <description>genotype calls and intensities to VCF</description> |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
3 <requirements> | 6 <requirements> |
4 <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement> | 7 <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement> |
5 </requirements> | 8 </requirements> |
6 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
10 @PREPARE_ENV@ | |
7 #set text_outputs_dir = 'text_outputs' | 11 #set text_outputs_dir = 'text_outputs' |
8 export BCFTOOLS_PLUGINS=\$(dirname `which bcftools`)/../libexec/bcftools && | |
9 mkdir $text_outputs_dir && | 12 mkdir $text_outputs_dir && |
10 bcftools +\$BCFTOOLS_PLUGINS/affy2vcf.so | 13 bcftools +\$BCFTOOLS_PLUGINS/affy2vcf.so |
11 #if str($reference_genome_source_cond.reference_genome_source) == "history": | 14 #if str($reference_genome_source_cond.reference_genome_source) == "history": |
12 --fasta-ref '$reference_genome_source_cond.history_item' | 15 --fasta-ref '$reference_genome_source_cond.history_item' |
13 #else: | 16 #else: |
25 #if str($append_version) == "no": | 28 #if str($append_version) == "no": |
26 --no-version | 29 --no-version |
27 #end if | 30 #end if |
28 --output '$output' | 31 --output '$output' |
29 --output-type $output_type | 32 --output-type $output_type |
30 --threads \${GALAXY_SLOTS:-4} | 33 @THREADS@ |
31 ]]></command> | 34 ]]></command> |
32 <inputs> | 35 <inputs> |
33 <param name="annot" type="data" format="csv" label="Probeset annotation file" /> | 36 <param name="annot" type="data" format="csv" label="Probeset annotation file" /> |
34 <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" /> | 37 <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" /> |
35 <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" /> | 38 <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" /> |
74 <option value="u" selected="true">Uncompressed BCF</option> | 77 <option value="u" selected="true">Uncompressed BCF</option> |
75 <option value="b">Compressed BCF</option> | 78 <option value="b">Compressed BCF</option> |
76 </param> | 79 </param> |
77 </inputs> | 80 </inputs> |
78 <outputs> | 81 <outputs> |
79 <data name="output" format="vcf" /> | 82 <expand macro="vcf_output"/> |
80 <data name="output_gender_estimate" format="txt" label="${tool.name} (gender estimate) on ${on_string}"> | 83 <data name="output_gender_estimate" format="txt" label="${tool.name} (gender estimate) on ${on_string}"> |
81 <filter>output_gender_estimate_cond['output_gender_estimate'] == "yes"</filter> | 84 <filter>output_gender_estimate_cond['output_gender_estimate'] == "yes"</filter> |
82 </data> | 85 </data> |
83 </outputs> | 86 </outputs> |
84 <tests> | 87 <tests> |
114 * **Output apt-probeset-genotype gender estimate** - output apt-probeset-genotype gender estimate into an additional dataset. | 117 * **Output apt-probeset-genotype gender estimate** - output apt-probeset-genotype gender estimate into an additional dataset. |
115 * **Append version and command line to the header** - append version and command line to the header of the output VCF dataset. | 118 * **Append version and command line to the header** - append version and command line to the header of the output VCF dataset. |
116 * **Select format for output** - select one of uncompressed/compressed VCF/BCF. | 119 * **Select format for output** - select one of uncompressed/compressed VCF/BCF. |
117 </help> | 120 </help> |
118 <citations> | 121 <citations> |
122 <expand macro="citation1"/> | |
119 <citation type="bibtex"> | 123 <citation type="bibtex"> |
120 @misc{None, | 124 @misc{None, |
121 journal = {None}, | 125 journal = {None}, |
122 author = {Genovese, Giulio}, | 126 author = {Genovese, Giulio}, |
123 title = {None}, | 127 title = {None}, |