Mercurial > repos > ebi-gxa > ct_check_labels

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

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"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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ct_check_labels.xml	Fri Nov 27 13:37:20 2020 +0000
@@ -0,0 +1,45 @@
+<tool id="ct_check_labels" name="Cell types - check labels" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+     <description>filters non-alphanumeric characters from labels</description>
+    <macros>
+        <import>ct_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+
+        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}"
+
+        #if $label_field
+        --label-field "${label_field}"
+        #end if
+
+        ]]></command>
+        <inputs>
+            
+            <param type="data" name="input_file" label="Input File" multiple="true" format="txt" help="Input metadta file" />
+            <param type="text" name="label_field" label="Label Field" optional="true" help="Name of label field in metadata file">
+                <expand macro="sanitize_strings" />
+            </param>
+            <param type="boolean" name="condensed" checked="false" label="Condensed Metadata File" help="Are the supplied metadata files of condensed format?" /> 
+            <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" />
+            <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" />
+            <param type="boolean" name="avoid_lowercase" checked="false" label="Avoid Lowercaase" help="Should setting the labels to lowercase be skipped? Default: False" /> 
+
+        </inputs>
+        <outputs>
+            <data name="output_path" format="txt" />
+        </outputs>
+        <tests>
+        <test>
+            <param name="input_file" value="SDRFs/E-ENAD-27.condensed-sdrf.tsv" />
+            <param name="label_field" value="inferred cell type" />
+            <param name="condensed" value="TRUE" />
+            <output name="output_path" file="checked_SDRF.tsv" compare="sim_size" />
+        </test>
+    </tests>
+        <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>