diff countDifferences.xml @ 0:a9fb5e4abb2d draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/countDifferences.xml	Mon Sep 20 21:51:24 2021 +0000
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+<tool id="countdifferences" name="countDifferences tool" version="1.0.0">
+  <description>allows to compare sequences from a multi-Fasta alignment file by calculating differences (in bp) and percentage identity</description>
+
+<requirements>
+  <requirement type="package" version="1.7.2">perl-bioperl</requirement>
+  <!--<requirement type="package" version="3.27">perl-string-approx</requirement>-->
+</requirements>
+
+<command detect_errors="aggressive"><![CDATA[
+
+#import re
+        ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
+        ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
+            ## Add single quotes around each input file identifier
+            #set $_input_file = "'{}'".format($input.element_identifier)
+            ln -s '${input}' ${_input_file} &&
+
+
+        perl '$__tool_directory__/countDifferences.pl' $_input_file $output1 $output2
+
+
+
+]]></command>
+ <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output"  -->
+ <!-- ./nuclescore.sh ${named_input_files} > "$output" -->
+
+<inputs>
+  <param format="fasta" name="input" type="data" label="Multi-FASTA file: "/>
+  <!--<param name="char" type="text" area="false" value="N" label="Character to be removed from Multi-FASTA file:" help="Users can directly write the character to be removed without quotes" />-->
+</inputs>
+
+ <outputs>
+    <data format="tabular" name="output1" label="bp_differences.tsv "/>
+    <data format="tabular" name="output2" label="percentage_identity.tsv "/>
+ </outputs>
+
+<help><![CDATA[
+countDifferences.pl is a Perl script allowing to calculate differences (changes in bp) and sequences percentage identity from an aligned multi-Fasta file.
+
+Two resulting tables are produced:
+(i) a table containing a matrix with bp differences for each sequence;
+(ii) a table containing a matrix with percentage identity for each sequence
+
+This script belongs to the getSequenceInfo supplementary tools.
+
+- GitHub: https://github.com/karubiotools/getSequenceInfo/tree/master/supplementary_tools
+]]>
+</help>
+
+</tool>