Mercurial > repos > diodupima > phage_coast_search

annotate phage_coast_search.xml @ 0:fb0ce7937a85 draft

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"planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
author diodupima
date Thu, 15 Jul 2021 16:51:26 +0000
parents
children 6a33bad2db7f
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1 <tool id="phage_coast_search" name="PhageCOAST - Search" version="0.1.2">
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2 <description>Run a new job, and identify the closest proteomes</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <expand macro="requirements"/>
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8 </requirements>
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9 <command><![CDATA[
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10 coast
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11 @QUERY@
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12 "$db"
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13 --engine blast
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14 --inplace_workspace
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15 @AAI_FILTER@
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16 @OUTPUT@
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17 @QUERY_KEYWORDS@
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18 @OUTPUT_FORMAT@
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19 @BLAST_TAX_FILTER@
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20 @BLAST_ALN_OPTIONS@
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21 @GENERIC_ALN_OPTIONS@
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22 -w 'http://rosalind.di.uminho.pt:6082/'
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23 --email phage@coast.um
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24 ]]></command>
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25 <inputs>
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26 <expand macro="input_query" />
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27 <expand macro="merlin_db_selection"/>
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28 <expand macro="blast_taxon_filter"/>
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29 <expand macro="output_format"/>
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30 <expand macro="aai_filter"/>
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31 <section name="aln_adv" title="Advanced Alignment Settings" >
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32 <expand macro="blast_aln_options"/>
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33 <expand macro="generic_aln_options"/>
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34 </section>
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35 </inputs>
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36 <outputs>
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37 <expand macro="results_alignment"/>
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38 <expand macro="results_report"/>
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39 </outputs>
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40 <tests>
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41 </tests>
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42 <help>
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43
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44 @TIME_WARNING@
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45
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46 PhageCOAST
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47 ==========
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48
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49 @GENERAL_DESC@
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50
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51 PhageCOAST is COAST adapted for the Phage Toolkit. The current build uses BLASTp as the search backend tool.
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52
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53 @AAI_DESC@
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54 @TAX_FILTER_WARNING@
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55 @OUT_DESC@
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56
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57 </help>
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58 <citations>
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59 <expand macro="citations_coast"/>
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60 <expand macro="citations_blast"/>
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61 </citations>
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62 </tool>