Mercurial > repos > devteam > convert_characters

diff convert_characters.xml @ 3:042ed2d0a017 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 20:25:21 -0400
parents 8a53d7f02ce4
children
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line diff
--- a/convert_characters.xml	Tue Jul 21 14:17:34 2015 -0400
+++ b/convert_characters.xml	Mon Jul 06 20:25:21 2020 -0400
@@ -1,58 +1,66 @@
-<tool id="Convert characters1" name="Convert"  version="1.0.0">
-  <description>delimiters to TAB</description>
-  <command interpreter="python">convert_characters.py "${input}" "${convert_from}" "${out_file1}"</command>
-  <inputs>
-    <param name="convert_from" type="select" label="Convert all">
-      <option value="s">Whitespaces</option>
-      <option value="T">Tabs</option>
-      <!--<option value="Sp">Spaces</option>-->
-      <option value="Dt">Dots</option>
-      <option value="C">Commas</option>
-      <option value="D">Dashes</option>
-      <option value="U">Underscores</option>
-      <option value="P">Pipes</option>
-      <option value="Co">Colons</option>
-    </param>
-    <param format="txt" name="input" type="data" label="in Query"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="convert_from" value="s"/>
-      <param name="input" value="1.bed"/>
-      <output name="out_file1" file="eq-convert.dat"/>
-    </test>
-    <test>
-      <param name="convert_from" value="s"/>
-      <param name="input" value="a.txt"/>
-      <output name="out_file1" file="a.tab"/>
-    </test>
-  </tests>
-  <help>
-
-**What it does**
-
-Converts all delimiters of a specified type into TABs.  Consecutive characters are condensed. For example, if columns are separated by 5 spaces they will converted into 1 tab.
-
------
-
-**Example**
-
-- Input file::
-
-    chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
-    chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
-    chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
-    chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+
-
-- Converting all pipe delimiters of the above file to TABs will get::
-
-    chrX  151283558  151283724  NM_000808_exon_8_0_chrX_151283559_r  0  -
-    chrX  151370273  151370486  NM_000808_exon_9_0_chrX_151370274_r  0  -
-    chrX  151559494  151559583  NM_018558_exon_1_0_chrX_151559495_f  0  +
-    chrX  151564643  151564711  NM_018558_exon_2_0_chrX_151564644_f  0  +
-
-</help>
-</tool>
+<tool id="Convert characters1" name="Convert"  version="1.0.1">
+    <description>delimiters to TAB</description>
+    <requirements>
+        <requirement type="package" version="3.8">python</requirement>
+    </requirements>
+    <command>
+        python '$__tool_directory__/convert_characters.py'
+            '${input}'
+            '${convert_from}'
+            '${out_file1}'
+    </command>
+    <inputs>
+        <param name="convert_from" type="select" label="Convert all">
+            <option value="s">Whitespaces</option>
+            <option value="T">Tabs</option>
+            <!--<option value="Sp">Spaces</option>-->
+            <option value="Dt">Dots</option>
+            <option value="C">Commas</option>
+            <option value="D">Dashes</option>
+            <option value="U">Underscores</option>
+            <option value="P">Pipes</option>
+            <option value="Co">Colons</option>
+        </param>
+        <param format="txt" name="input" type="data" label="in Query"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="out_file1" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="convert_from" value="s"/>
+            <param name="input" value="1.bed"/>
+            <output name="out_file1" file="eq-convert.dat"/>
+        </test>
+        <test>
+            <param name="convert_from" value="s"/>
+            <param name="input" value="a.txt"/>
+            <output name="out_file1" file="a.tab"/>
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Converts all delimiters of a specified type into TABs.  Consecutive characters are condensed. For example, if columns are separated by 5 spaces they will converted into 1 tab.
+
+-----
+
+**Example**
+
+- Input file::
+
+    chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
+    chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
+    chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
+    chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+
+
+- Converting all pipe delimiters of the above file to TABs will get::
+
+    chrX  151283558  151283724  NM_000808_exon_8_0_chrX_151283559_r  0  -
+    chrX  151370273  151370486  NM_000808_exon_9_0_chrX_151370274_r  0  -
+    chrX  151559494  151559583  NM_018558_exon_1_0_chrX_151559495_f  0  +
+    chrX  151564643  151564711  NM_018558_exon_2_0_chrX_151564644_f  0  +
+
+    </help>
+</tool>