Mercurial > repos > mvdbeek > add_input_name_as_column

changeset 6:3284b72eef56 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
author iuc
date Wed, 25 Mar 2020 07:11:05 -0400
parents 06061aa49527
children
files add_input_name_as_column.py add_input_name_as_column.xml test-data/signature_without_header.tab
diffstat 3 files changed, 86 insertions(+), 79 deletions(-) [+]
line wrap: on
line diff
--- a/add_input_name_as_column.py	Wed Mar 06 09:16:29 2019 -0500
+++ b/add_input_name_as_column.py	Wed Mar 25 07:11:05 2020 -0400
@@ -1,5 +1,5 @@
+import argparse
 import io
-import argparse
 
 
 def Parser():
@@ -8,6 +8,8 @@
     the_parser.add_argument('--output', required=True, action="store", type=str, help="output file path")
     the_parser.add_argument('--label', required=True, action="store", type=str, help="label to add in last column")
     the_parser.add_argument('--header', action="store", type=str, help="column label for last column")
+    the_parser.add_argument('--prepend', action='store_true', default=False, help='Prepend column instead of appending' )
+
     args = the_parser.parse_args()
     return args
 
@@ -19,7 +21,11 @@
     for i, line in enumerate(input):
         line = line.strip('\n')
         if (i == 0) and args.header:
-            line = "%s\t%s\n" % (line, args.header)
+            new_entry = args.header
         else:
-            line = "%s\t%s\n" % (line, args.label)
+            new_entry = args.label
+        if args.prepend:
+            line = "%s\t%s\n" % (new_entry, line)
+        else:
+            line = "%s\t%s\n" % (line, new_entry)
         output.write(line)
--- a/add_input_name_as_column.xml	Wed Mar 06 09:16:29 2019 -0500
+++ b/add_input_name_as_column.xml	Wed Mar 25 07:11:05 2020 -0400
@@ -1,9 +1,9 @@
-<tool id="addName" name="Add input name as column" version="0.1.2" profile="17.09">
-  <description>to an existing tabular file</description>
-  <requirements>
-    <requirement type="package" version="3.7">python</requirement>
-  </requirements>
-  <command><![CDATA[
+<tool id="addName" name="Add input name as column" version="0.2.0" profile="17.09">
+    <description>to an existing tabular file</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+    <command><![CDATA[
 python '$__tool_directory__/'add_input_name_as_column.py
 --input '$input'
 --label '$input.element_identifier'
@@ -11,51 +11,52 @@
 #if $header.contains_header=="yes":
   --header "$header.colname"
 #end if
-  ]]></command>
-  <inputs>
-  <param format="txt" name="input" type="data" label="to Dataset" help="Dataset missing? See TIP below" />
-  <conditional name="header">
-    <param name="contains_header" type="select" label="input contains a header line?" >
-      <option value="yes" selected="true">Yes</option>
-      <option value="no">No</option>
-    </param>
-    <when value="yes">
-      <param name="colname" type="text" value="sample" help="select a column header to be added in the first line">
-        <validator type="empty_field" message="please add a column header"/>
-      </param>
-    </when>
-    <when value="no">
-    </when>
-  </conditional>
-  </inputs>
-  <outputs>
-    <data name="output" format="tabular" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" value="signature.tab" ftype="tabular" />
-      <param name="contains_header" value="yes" />
-      <param name="colname" value="sample" />
-      <output name="output" file="signature_with_header.tab" ftype="tabular"/>
-    </test>
-    <test>
-      <param name="input" value="signature.tab" ftype="tabular" />
-      <param name="contains_header" value="no" />
-      <output name="output" file="signature_without_header.tab" ftype="tabular"/>
-    </test>
-  </tests>
-  <help>
+$prepend 
+    ]]></command>
+    <inputs>
+        <param format="txt" name="input" type="data" label="to Dataset" help="Dataset missing? See TIP below" />
+        <conditional name="header">
+            <param name="contains_header" type="select" label="input contains a header line?" >
+                <option value="yes" selected="true">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param name="colname" type="text" value="sample" help="select a column header to be added in the first line">
+                    <validator type="empty_field" message="please add a column header"/>
+                </param>
+            </when>
+            <when value="no"/>
+        </conditional>
+        <param name="prepend" type="boolean" truevalue="--prepend" falsevalue="" checked="false" label="Prepend the colum" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="signature.tab" ftype="tabular" />
+            <param name="contains_header" value="yes" />
+            <param name="colname" value="sample" />
+            <output name="output" file="signature_with_header.tab" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="signature.tab" ftype="tabular" />
+            <param name="contains_header" value="no" />
+            <param name="prepend" value="true" />
+            <output name="output" file="signature_without_header.tab" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Adds a new column with the name of the input file as it appears in the history.
+By default the column is appended.
+
+-----
 
 .. class:: infomark
 
-**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
-
------
-
-**What it does**
+**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
 
-Adds a new column with the name of the input file as it appears in the history.
-Written by Marius van den Beek, m.vandenbeek at gmail dot com
-  </help>
+    ]]></help>
 </tool>
-
--- a/test-data/signature_without_header.tab	Wed Mar 06 09:16:29 2019 -0500
+++ b/test-data/signature_without_header.tab	Wed Mar 25 07:11:05 2020 -0400
@@ -1,27 +1,27 @@
-overlap	num of pairs	probability	signature.tab
-1	8	0.000028	signature.tab
-2	7	0.000019	signature.tab
-3	9	0.000034	signature.tab
-4	6	0.000014	signature.tab
-5	8	0.000020	signature.tab
-6	10	0.000086	signature.tab
-7	6	0.000030	signature.tab
-8	9	0.000038	signature.tab
-9	12	0.000058	signature.tab
-10	24	0.000094	signature.tab
-11	11	0.000071	signature.tab
-12	9	0.000058	signature.tab
-13	8	0.000029	signature.tab
-14	11	0.000042	signature.tab
-15	13	0.000112	signature.tab
-16	8	0.000070	signature.tab
-17	11	0.000066	signature.tab
-18	12	0.000697	signature.tab
-19	13	0.000085	signature.tab
-20	5	0.000015	signature.tab
-21	18	0.000540	signature.tab
-22	9	0.000030	signature.tab
-23	8	0.000036	signature.tab
-24	7	0.000037	signature.tab
-25	14	0.000058	signature.tab
-26	12	0.000050	signature.tab
+signature.tab	overlap	num of pairs	probability
+signature.tab	1	8	0.000028
+signature.tab	2	7	0.000019
+signature.tab	3	9	0.000034
+signature.tab	4	6	0.000014
+signature.tab	5	8	0.000020
+signature.tab	6	10	0.000086
+signature.tab	7	6	0.000030
+signature.tab	8	9	0.000038
+signature.tab	9	12	0.000058
+signature.tab	10	24	0.000094
+signature.tab	11	11	0.000071
+signature.tab	12	9	0.000058
+signature.tab	13	8	0.000029
+signature.tab	14	11	0.000042
+signature.tab	15	13	0.000112
+signature.tab	16	8	0.000070
+signature.tab	17	11	0.000066
+signature.tab	18	12	0.000697
+signature.tab	19	13	0.000085
+signature.tab	20	5	0.000015
+signature.tab	21	18	0.000540
+signature.tab	22	9	0.000030
+signature.tab	23	8	0.000036
+signature.tab	24	7	0.000037
+signature.tab	25	14	0.000058
+signature.tab	26	12	0.000050