Mercurial > repos > gga > chado_expression_add_expression

comparison expression_add_expression.xml @ 7:126fc4d52d4e draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
author gga
date Wed, 21 Aug 2019 05:10:30 -0400
parents 546ea3a2a7f7
children
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6:546ea3a2a7f7 7:126fc4d52d4e
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="expression_add_expression" name="Chado expression add" version="@WRAPPER_VERSION@.1"> 2 <tool id="expression_add_expression" name="Chado expression add" version="@WRAPPER_VERSION@">
3 <description></description> 3 <description></description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
12 chakin expression add_expression 12 chakin expression add_expression
13 '$organism_id' 13 '$organism_id'
14 '$analysis_id' 14 '$analysis_id'
15 '$file_path' 15 '$file_path'
16 16
17 #if $unit:
18 --unit '$unit'
19 #end if
20
21 --query_type '$query_type'
22
23 $match_on_name
24
25 #if $re_name:
26 --re_name '$re_name'
27 #end if
28
29 $skip_missing
30
17 > '$results' 31 > '$results'
18 32
19 @ZIP_PSQL@ 33 @ZIP_PSQL@
20 ]]></command> 34 ]]></command>
21 <inputs> 35 <inputs>
22 <expand macro="psql_target"/> 36 <expand macro="psql_target"/>
23 <!-- arguments --> 37 <!-- arguments -->
24 <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" /> 38 <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
25 <param argument="analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" /> 39 <param argument="analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" />
26 <param name="file_path" label="Expression matrix" argument="file_path" type="data" format="tabular" help="Tabular file where columns are experimental conditions, and rows are features" /> 40 <param name="file_path" label="Expression matrix" argument="file_path" type="data" format="tabular" help="Tabular file where columns are experimental conditions, and rows are features" />
41
42 <param name="unit" label="Unit" argument="--unit" type="text" help="The units associated with the loaded values (ie, FPKM, RPKM, raw counts)" />
43
44 <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="mRNA" />
45
46 <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" />
47
48 <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">
49 <expand macro="sanitized"/>
50 </param>
51
52 <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." />
27 53
28 <expand macro="wait_for"/> 54 <expand macro="wait_for"/>
29 </inputs> 55 </inputs>
30 <outputs> 56 <outputs>
31 <data format="txt" name="results"/> 57 <data format="txt" name="results"/>