diff subtract_query.xml @ 0:5f6ebef89722 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/subtract_query.xml	Tue Apr 01 10:51:41 2014 -0400
@@ -0,0 +1,131 @@
+<tool id="subtract_query1" name="Subtract Whole Dataset" version="0.1">
+  <description>from another dataset</description>
+  <requirements>
+    <requirement type="package" version="0.7.1">bx-python</requirement>
+    <requirement type="package" version="1.0.0">galaxy-ops</requirement>
+  </requirements>
+  <command interpreter="python">
+    subtract_query.py $input1 $input2 $begin_col $end_col $output
+    #if str($ignore_empty_end_cols) == 'true':
+      --ignore-empty-end-cols
+    #end if
+
+  </command>
+  <inputs>
+    <param format="txt" name="input2" type="data" label="Subtract" help="Second dataset" />
+    <param format="txt" name="input1" type="data" label="from" help="First dataset" />
+    <param name="begin_col" type="data_column" data_ref="input1" force_select="False" label="Restrict subtraction between 'begin column'" />
+    <param name="end_col" type="data_column" data_ref="input1" force_select="False" label="and 'end column'" help="Specifying columns for restricting subtraction is available only for tabular formatted datasets" />
+    <param name="ignore_empty_end_cols" type="boolean" label="Ignore empty columns and whitespace at end of line when subtracting"/>
+  </inputs>
+  <outputs>
+    <data format="input" name="output" metadata_source="input1" />
+  </outputs>
+  <tests>
+  	<!-- Subtract 2 non-tabular files with no column restrictions. -->
+  	<!-- Cannot figure out why this test won't pass, it works in real time... -->
+  	<!--
+    <test>
+      <param name="input1" value="1.txt" />
+      <param name="input2" value="2.txt" />
+      <param name="begin_col" value="None" />
+      <param name="end_col" value="None" />
+      <output name="output" file="subtract-query-1.dat" />
+    </test>
+    -->
+  	<!-- Subtract 2 tabular files with no column restrictions. -->
+    <test>
+      <param name="input1" value="eq-showbeginning.dat" />
+      <param name="input2" value="eq-showtail.dat" />
+      <param name="begin_col" value="None" />
+      <param name="end_col" value="None" />
+      <output name="output" file="subtract-query-2.dat" />
+    </test>
+  	<!-- Subtract 2 tabular files with column restrictions. -->
+    <test>
+      <param name="input1" value="eq-showbeginning.dat" />
+      <param name="input2" value="eq-removebeginning.dat" />
+      <param name="begin_col" value="c1" />
+      <param name="end_col" value="c3" />
+      <output name="output" file="subtract-query-3.dat" />
+    </test>
+  	<!-- Subtract a non-tabular file from a tabular file with no column restrictions. -->
+    <test>
+      <param name="input1" value="eq-showbeginning.dat" />
+      <param name="input2" value="2.txt" />
+      <param name="begin_col" value="None" />
+      <param name="end_col" value="None" />
+      <output name="output" file="subtract-query-4.dat" />
+    </test>
+    <!-- Subtract  2 tabular files with no column restrictions, ignoring empty end columns. -->
+    <test>
+      <param name="input1" value="eq-showbeginning_e.dat" />
+      <param name="input2" value="eq-showtail.dat" />
+      <param name="begin_col" value="None" />
+      <param name="end_col" value="None" />
+      <param name="ignore_empty_end_cols" value="true" />
+      <output name="output" file="subtract-query-2.dat" />
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**TIP:** This tool complements the tool in the **Operate on Genomic Intervals** tool set which subtracts the intervals of two datasets.
+
+
+-----
+
+**Syntax**
+
+This tool subtracts an entire dataset from another dataset.  
+
+- Any text format is valid.
+- If both dataset formats are tabular, you may restrict the subtraction to specific columns **contained in both datasets** and the resulting dataset will include only the columns specified. 
+- The begin column must be less than or equal to the end column.  If it is not, begin column is switched with end column.
+- If begin column is specified but end column is not, end column will default to begin_column (and vice versa).
+- All blank and comment lines are skipped and not included in the resulting dataset (comment lines are lines beginning with a # character).
+- Duplicate lines are eliminated from both dataset prior to subtraction.  If any duplicate lines were eliminated from the first dataset, the number is displayed in the resulting history item.
+
+-----
+
+**Example**
+
+If this is the **First dataset**::
+
+  chr1            4225    19670
+  chr10           6       8
+  chr1            24417   24420
+  chr6_hla_hap2   0       150
+  chr2            1       5
+  chr10           2       10
+  chr1            30      55
+  chrY            1       20
+  chr1            1225979 42287290
+  chr10           7       8 
+
+and this is the **Second dataset**::
+
+  chr1            4225    19670
+  chr10           6       8
+  chr1            24417   24420
+  chr6_hla_hap2   0       150
+  chr2            1       5
+  chr1            30      55
+  chrY            1       20
+  chr1            1225979 42287290
+
+Subtracting the **Second dataset** from the **First dataset** (including all columns) will yield::
+
+  chr10           7       8 
+  chr10           2       10
+
+Conversely, subtracting the **First dataset** from the **Second dataset** (including all columns) will result in an empty dataset.
+
+Subtracting the **Second dataset** from the **First dataset** (restricting to columns c1 and c2) will yield::
+
+  chr10           7
+  chr10           2
+
+  </help>
+</tool>
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