Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

annotate data_manager/customProDB_annotation.xml @ 9:9fec6c7f46eb draft

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author galaxyp
date Fri, 13 Jan 2017 12:18:39 -0500
parents a0ca66b32792
children a0a5aa56d29c
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9fec6c7f46eb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
galaxyp
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1 <tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="0.0.1">
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2 <description>builder</description>
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3 <command interpreter="Rscript --vanilla">customProDB_annotation.R
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4 --outputFile "${out_file}"
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5 --dbkey "${dbkey}"
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6 --dbsnp "${dbsnp}"
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7 #if $cosmic
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8 --cosmic true
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9 #end if
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10 --dbkey_description ${ dbkey.get_display_text() }
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11 2&gt;&amp;1
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12 </command>
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13 <stdio>
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14 <exit_code range=":-1" />
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15 <exit_code range="1:" />
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16 </stdio>
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17 <inputs>
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18 <param type="genomebuild" name="dbkey" value="" label="UCSC dbKey for reference genome" />
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19 <param type="text" name="dbsnp" value="" label="dbSNP identifier currently available from UCSC" help="e.g. 'snp142'" />
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20 <param type="boolean" name="cosmic" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
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21 </inputs>
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22 <outputs>
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23 <data name="out_file" format="data_manager_json"/>
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24 </outputs>
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25
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26 <help>
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28 .. class:: infomark
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9fec6c7f46eb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 7115cf54f290b51b6a791f9ae288dd907a31fb0a
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30 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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31
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32 </help>
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33 <citations>
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34 <citation type="doi">10.1093/bioinformatics/btt543</citation>
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35 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
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36 year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
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37 </citations>
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38 </tool>