Mercurial > repos > ebi-gxa > ct_check_labels

comparison ct_check_labels.xml @ 0:733ef9ca2455 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:37:20 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:733ef9ca2455
1 <tool id="ct_check_labels" name="Cell types - check labels" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>filters non-alphanumeric characters from labels</description>
3 <macros>
4 <import>ct_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8
9 check_labels.R --input-file "${input_file}" --condensed "${condensed}" --attribute-type-col-num "${attribute_type_col_num}" --variable-col-num "${variable_col_num}" --avoid-lowercase "${avoid_lowercase}" --output-path "${output_path}"
10
11 #if $label_field
12 --label-field "${label_field}"
13 #end if
14
15 ]]></command>
16 <inputs>
17
18 <param type="data" name="input_file" label="Input File" multiple="true" format="txt" help="Input metadta file" />
19 <param type="text" name="label_field" label="Label Field" optional="true" help="Name of label field in metadata file">
20 <expand macro="sanitize_strings" />
21 </param>
22 <param type="boolean" name="condensed" checked="false" label="Condensed Metadata File" help="Are the supplied metadata files of condensed format?" />
23 <param type="integer" name="attribute_type_col_num" value='5' label="Number of Attribute Type Column" help="Number of the attribute type field in condensed metadata file. Default: 5" />
24 <param type="integer" name="variable_col_num" value='6' label="Number of Label Column" help="Number of the label field in condensed metadata file. Default: 6" />
25 <param type="boolean" name="avoid_lowercase" checked="false" label="Avoid Lowercaase" help="Should setting the labels to lowercase be skipped? Default: False" />
26
27 </inputs>
28 <outputs>
29 <data name="output_path" format="txt" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="input_file" value="SDRFs/E-ENAD-27.condensed-sdrf.tsv" />
34 <param name="label_field" value="inferred cell type" />
35 <param name="condensed" value="TRUE" />
36 <output name="output_path" file="checked_SDRF.tsv" compare="sim_size" />
37 </test>
38 </tests>
39 <help><![CDATA[
40 @HELP@
41
42 @VERSION_HISTORY@
43 ]]></help>
44 <expand macro="citations" />
45 </tool>