Mercurial > repos > galaxyp > custom_pro_db

comparison customProDB.xml @ 11:982fb2cde6c5 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
author galaxyp
date Fri, 13 Jan 2017 12:18:32 -0500
parents ed65d110c1b5
children 2656b09d2046
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10:ed65d110c1b5 11:982fb2cde6c5
64 </param> 64 </param>
65 <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" /> 65 <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" />
66 <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" /> 66 <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
67 </when> 67 </when>
68 <when value="history"> 68 <when value="history">
69 <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" /> 69 <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
70 <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" /> 70 <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />
71 <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" /> 71 <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />
72 <param name="ids" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" /> 72 <param name="ids" type="data" format="RData" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" />
73 <param name="bamInput" type="data" format="bam" label="BAM file"> 73 <param name="bamInput" type="data" format="bam" label="BAM file">
74 <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> 74 <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
75 </param> 75 </param>
76 <param name="baiInput" type="data" format="bam_index" label="BAM Index file"> 76 <param name="baiInput" type="data" format="bam_index" label="BAM Index file">
77 <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> 77 <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
103 </test> 103 </test>
104 </tests> 104 </tests>
105 <help> 105 <help>
106 **Description** 106 **Description**
107 107
108 Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). 108 Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). </help>
109 </help> 109 <citations>
110 <citation type="doi">10.1093/bioinformatics/btt543</citation>
111 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub
112 repository},
113 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit =
114 {$sha1$}" -->
115 </citations>
110 </tool> 116 </tool>