Mercurial > repos > galaxyp > custom_pro_db

comparison customProDB.xml @ 19:14b5405f898a draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 380011a7d342f3c7a2780dfa841adca1f6df1d30
author galaxyp
date Fri, 22 Feb 2019 02:12:57 -0500
parents c429c2baecb8
children
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equal deleted inserted replaced
18:88e4cea5171e 19:14b5405f898a
1 <tool id="custom_pro_db" name="CustomProDB" version="1.16.1.0"> 1 <tool id="custom_pro_db" name="CustomProDB" version="1.22.0">
2 <description>Generate protein FASTAs from exosome or transcriptome data</description> 2 <description>Generate protein FASTAs from exosome or transcriptome data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.3.1">r-base</requirement> 4 <!--<requirement type="package" version="1.22.0">bioconductor-customprodb</requirement>-->
5 <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>--> 5 <requirement type="package" version="1.26.0">bioconductor-rgalaxy</requirement>
6 <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement> 6 <requirement type="package" version="1.28.3">bioconductor-variantannotation</requirement>
7 <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement> 7 <requirement type="package" version="2.0.1">r-devtools</requirement>
8 <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement> 8 <requirement type="package" version="2.0.1">r-testthat</requirement>
9 <requirement type="package" version="1.26.4">bioconductor-genomicfeatures</requirement> 9 <requirement type="package" version="0.1.7">r-getoptlong</requirement>
10 <requirement type="package" version="1.11.1">r-devtools</requirement> 10 <requirement type="package" version="1.12.0">r-data.table</requirement>
11 <requirement type="package" version="3.98_1.4">r-xml</requirement> 11 <requirement type="package" version="0.4_11">r-sqldf</requirement>
12 <requirement type="package" version="0.10.11">r-rmysql</requirement>
13 <requirement type="package" version="1.0.2">r-testthat</requirement>
14 <requirement type="package" version="0.1.0">r-getoptlong</requirement>
15 <requirement type="package" version="1.1.2">r-stringi</requirement>
16 <requirement type="package" version="1.1.0">r-stringr</requirement>
17 <requirement type="package" version="1.10.0">r-data.table</requirement>
18 <requirement type="package" version="0.4_10">r-sqldf</requirement>
19 <requirement type="package" version="0.6_6">r-gsubfn</requirement>
20 <requirement type="package" version="2.3_47">r-chron</requirement>
21 <requirement type="package" version="0.3_10">r-proto</requirement>
22 <requirement type="package" version="1.8.4">r-plyr</requirement> 12 <requirement type="package" version="1.8.4">r-plyr</requirement>
13 <requirement type="package" version="0.10.13">r-rmysql</requirement>
23 </requirements> 14 </requirements>
24 <stdio> 15 <stdio>
25 <exit_code range="1:" level="fatal" description="Job Failed" /> 16 <exit_code range="1:" level="fatal" description="Job Failed" />
26 </stdio> 17 </stdio>
27 <command><![CDATA[ 18 <command><![CDATA[
159 <param name="outputIndels" value="--outputIndels" /> 150 <param name="outputIndels" value="--outputIndels" />
160 <param name="outputSQLite" value="--outputSQLite" /> 151 <param name="outputSQLite" value="--outputSQLite" />
161 <output name="output_rpkm" file="hg19_rpkm0.fasta" /> 152 <output name="output_rpkm" file="hg19_rpkm0.fasta" />
162 <output name="output_snv" file="hg19_dbsnp_snv.fasta" /> 153 <output name="output_snv" file="hg19_dbsnp_snv.fasta" />
163 <output name="output_indel" file="hg19_indel.fasta" /> 154 <output name="output_indel" file="hg19_indel.fasta" />
164 <output name="output_variant_annotation_rdata" file="hg19_dbsnp_variant_annotation.rdata" /> 155 <output name="output_genomic_mapping_sqlite" file="hg19_dbsnp_genomic_mapping.sqlite" />
165 <output name="output_variant_annotation_sqlite" file="hg19_dbsnp_variant_annotation.sqlite" /> 156 <output name="output_variant_annotation_sqlite" file="hg19_dbsnp_variant_annotation.sqlite" />
166 </test> 157 </test>
167 <test expect_num_outputs="3"> 158 <test expect_num_outputs="3">
168 <param name="bamInput" value="hg19/test1_sort.bam" dbkey="hg19" /> 159 <param name="bamInput" value="hg19/test1_sort.bam" dbkey="hg19" />
169 <param name="vcfInput" value="hg19/test1.vcf" dbkey="hg19" /> 160 <param name="vcfInput" value="hg19/test1.vcf" dbkey="hg19" />