annotate coast_report.xml @ 1:3f1f00433c2b draft

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author diodupima
date Wed, 17 Nov 2021 11:09:46 +0000
parents 44bd59ba0858
children e816ffbcf425
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1 <tool id="coast_report" name="COAST - Report generator" version="0.1.2">
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2 <description>Recreate the report and outputs with different settings</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 report
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11 "$result_file"
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12 @QUERY@
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13 @AAI_FILTER@
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14 @HYPO_FILTER@
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15 @OUTPUT@
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16 @QUERY_KEYWORDS@
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17 @OUTPUT_FORMAT@
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18 ]]></command>
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19 <inputs>
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20 <!--Select the kind of input to be used-->
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21 <expand macro="input_query" />
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22 <param name="result_file" type="data" format="tabular" label="Load previous COAST generated alignment file"/>
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23 <!--Outputs selection-->
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24 <expand macro="output_format"/>
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25 <!--AAI filtering score-->
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26 <expand macro="aai_filter"/>
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27 <expand macro="hypothetical_filter"/>
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28 </inputs>
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29 <outputs>
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30 <expand macro="results_report"/>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="query_file" value="protein.faa" />
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35 <param name="result_file" value="blast_results.tab" />
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36 <param name="aai" value="10" />
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37 <param name="min_cov" value="50" />
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38 <param name="min_id" value="40" />
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39 <!-- <output name="coast_report" file="report/coast_report.html" lines_diff="4"/>-->
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40 <output name="bh_results" file="report/bh_results.tab" />
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41 <output name="coast_results" file="report/coast_results.tab" />
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42 </test>
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43 <test>
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44 <param name="query_file" value="protein.faa" />
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45 <param name="result_file" value="blast_results.tab" />
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46 <param name="aai" value="20" />
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47 <param name="min_cov" value="30" />
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48 <param name="min_id" value="30" />
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49 <param name="hypothetical" value="true" />
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50 <!-- <output name="coast_report" file="report_h/coast_report.html" lines_diff="4"/>-->
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51 <output name="bh_results" file="report_h/bh_results.tab" />
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52 <output name="coast_results" file="report_h/coast_results.tab" />
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53 </test>
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54 </tests>
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55 <help>
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56
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57 @HYPO_FILTER_WARNING@
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58
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59 COAST Report
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60 ============
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61
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62 Generate COAST reports and outputs based in different parameters, using the tabular alignment output produced by COAST Search jobs.
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63
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64 @GENERAL_DESC@
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65 @AAI_DESC@
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66 @OUT_DESC@
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67
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68 </help>
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69 <citations>
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70 <expand macro="citations_coast"/>
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71 </citations>
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72 </tool>