diff column_regex_substitution.xml @ 0:12b740c4cbc1 draft default tip

planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/column_regex_substitution.xml	Fri Sep 07 10:29:30 2018 -0400
@@ -0,0 +1,57 @@
+<tool id="column_regex_substitution" name="Column substitution" version="0.0.1">
+    <description>by regular expressions</description>
+    <requirements>
+        <requirement type="package" version="2.7">python</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <version_command>python column_regex_substitution.py --version</version_command>
+    <command><![CDATA[
+        #import pipes
+        python '$__tool_directory__/column_regex_substitution.py'
+        --input '${input_tabular}'
+        --pattern ${pipes.quote( str( $pattern ).replace('\\','\\\\').decode( 'string_escape' ) ) or '""'}
+        --replacement ${ pipes.quote( str( $replacement ).replace('\\','\\\\').decode( 'string_escape' ) ) or '""' }
+        --columns '${ $columns or "" }'
+        --output '${outfile}'
+        #if $input_tabular.metadata.delimiter:
+            --delimiter ${ pipes.quote( str( $input_tabular.unsanitized.metadata.delimiter ) ) }
+        #end if
+        --column_offset '-1'
+    ]]>
+    </command>
+    <inputs>
+        <param name="input_tabular" type="data" format="txt" label="File to perform substitution on" />
+        <param name="pattern" type="text" label="Pattern to Match">
+            <sanitizer sanitize="False" />
+        </param>
+        <param name="replacement" type="text" label="Replacement">
+            <sanitizer sanitize="False" />
+        </param>
+        <param name="columns" label="Columns for substitution" type="data_column" data_ref="input_tabular" optional="True" multiple="True" help="Selecting no columns will target all columns"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format_source="input_tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_tabular" ftype="tabular" value="column_regex_substitution_in.tabular"/>
+            <param name="pattern" value="^$"/>
+            <param name="replacement" value="."/>
+            <param name="columns" value="1"/>
+            <output name="outfile" ftype="tabular" file="column_regex_substitution_out.tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Use regular expressions (regex) to substitute field values. Datasets that do not have a metadata delimiter value will be treated as a single column per row.
+
+This tool makes use of Python's `re.sub functionality <https://docs.python.org/2/library/re.html#re.sub>`_.
+
+]]>
+    </help>
+<citations></citations>
+</tool>