Mercurial > repos > gga > chado_load_blast

annotate load_blast.xml @ 4:08ae8b27b193 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0a8b62b6cdce301067cba25d30171d5f6ec04f40"
author gga
date Wed, 09 Dec 2020 14:22:29 +0000
parents f23cfcb0ab8c
children
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1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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1 <?xml version="1.0"?>
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2 <tool id="load_blast" name="Chado load Blast results" version="@WRAPPER_VERSION@">
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3 <description></description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <code file="chado.py"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 @START_PSQL@ &&
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1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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12 chakin load blast
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13 '$analysis_id'
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14 '$organism_id'
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15 '$input'
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16
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17 --blastdb_id '$blastdb_id'
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19 --query_type '$query_type'
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21 $match_on_name
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23 #if $re_name:
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24 --re_name '$re_name'
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25 #end if
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27 $skip_missing
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28
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29 | jq -S . > $results
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31 @ZIP_PSQL@
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32 ]]></command>
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33 <inputs>
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34 <expand macro="psql_target"/>
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35 <!-- arguments -->
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36 <param name="input" label="Blast results" argument="input" type="data" format="xml" help="Path to the Blast XML file to load" />
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37 <param argument="analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" />
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38 <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
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40 <!-- options -->
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41 <param name="query_type" label="Query type" argument="--query_type" type="text" help="The feature type (e.g. 'gene', 'mRNA', 'polypeptide', 'contig') of the query. It must be a valid Sequence Ontology term." value="polypeptide" />
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43 <param name="match_on_name" label="Match On Name" argument="--match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match features using their name instead of their uniquename" />
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45 <param argument="blastdb_id" type="select" dynamic_options="list_dbs()" label="Database blasted against" />
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47 <param name="re_name" label="Name regular expression" argument="--re_name" type="text" help="Regular expression to extract the feature name from the input file (first capturing group will be used)." optional="true">
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48 <expand macro="sanitized"/>
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49 </param>
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51 <param name="skip_missing" label="Skip Missing" argument="--skip_missing" type="boolean" truevalue="--skip_missing" falsevalue="" help="Skip lines with unknown features instead of aborting everything." />
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52
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53 <expand macro="wait_for"/>
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54 </inputs>
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55 <outputs>
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56 <data format="json" name="results"/>
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57 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
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58 <filter>psql_target['method'] == "pgtools"</filter>
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59 </data>
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60 </outputs>
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61 <help>
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62 Load a blast analysis, in the same way as does the tripal_analysis_blast module
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63
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64 @HELP@
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65 </help>
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66 </tool>