Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced

diff fastx_barcode_splitter.xml @ 4:0fb7e9130a70 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
author lparsons
date Mon, 02 May 2016 17:04:32 -0400
parents e7b7cdc1834d
children
line wrap: on
line diff
--- a/fastx_barcode_splitter.xml	Fri Mar 11 17:24:31 2016 -0500
+++ b/fastx_barcode_splitter.xml	Mon May 02 17:04:32 2016 -0400
@@ -1,82 +1,86 @@
-<tool id="cshl_princeton_fastx_barcode_splitter" version="1.1" name="Barcode Splitter">
-	<description></description>
-	<command interpreter="bash"><![CDATA[
+<tool id="cshl_princeton_fastx_barcode_splitter" version="1.2" name="Barcode Splitter">
+  <description></description>
+  <command interpreter="bash" detect_errors="aggressive"><![CDATA[
 fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "split/" $input.extension --mismatches $mismatches --partial $partial
 #if $refBarcodeLocation.barcodeLocation == "idxfile":
     --idxfile $refBarcodeLocation.idxfile
 #else:
     $refBarcodeLocation.EOL
 #end if
-> $output
+> $summary
 ]]>
-	</command>
+  </command>
 
-	<inputs>
-		<param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
-		<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
+  <inputs>
+    <param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
+    <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
 
-		<conditional name="refBarcodeLocation">
-			<param name="barcodeLocation" type="select" label="Barcodes found at">
-				<option value="bol">Start of sequence (5' end)</option>
-				<option value="eol">End of sequence (3' end)</option>
-				<option value="idxfile">Separate index file</option>
-			</param>
-			<when value="bol">
-				<param name="EOL" type="hidden" value="--bol" />
-			</when>
-			<when value="eol">
-				<param name="EOL" type="hidden" value="--eol" />
-			</when>
-			<when value="idxfile">
-				<param name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
-			</when>
-		</conditional>
+    <conditional name="refBarcodeLocation">
+      <param name="barcodeLocation" type="select" label="Barcodes found at">
+        <option value="bol">Start of sequence (5' end)</option>
+        <option value="eol">End of sequence (3' end)</option>
+        <option value="idxfile">Separate index file</option>
+      </param>
+      <when value="bol">
+        <param name="EOL" type="hidden" value="--bol" />
+      </when>
+      <when value="eol">
+        <param name="EOL" type="hidden" value="--eol" />
+      </when>
+      <when value="idxfile">
+        <param name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
+      </when>
+    </conditional>
 
-		<param name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" />
+    <param name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" />
 
-		<param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
+    <param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
 
-	</inputs>
+  </inputs>
 
-	<outputs>
-        <data format="html" name="output">
-            <discover_datasets pattern="__designation_and_ext__" directory="split" visible="true" label="${tool.name}: ${designation}"/>
-        </data>
-	</outputs>
+  <outputs>
+    <data format="tabular" name="summary" label="${tool.name} on ${on_string}: Summary" />
+    <collection name="split_output" type="list" format_source="input" label="${tool.name} on ${on_string}">
+      <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false" label="${designation}"/>
+    </collection>
+  </outputs>
 
-    <tests>
-		<test>
-			<!-- Split a FASTQ file -->
-			<param name="BARCODE" value="fastx_barcode_splitter1.txt" />
-			<param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
-			<param name="barcodeLocation" value="bol" />
-			<param name="mismatches" value="2" />
-			<param name="partial" value="0" />
-            <output name="output" file="fastx_barcode_splitter1.out">
-                <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
-                <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
-                <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
-                <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
-                <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
-            </output>
-		</test>
-		<test>
-			<!-- Split a FASTQ file, using separate index read -->
-			<param name="BARCODE" value="fastx_barcode_splitter1.txt" />
-			<param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
-			<param name="idxfile" value="fastx_barcode_splitter_index.fastq" ftype="fastqsolexa" />
-			<param name="barcodeLocation" value="idxfile" />
-			<param name="mismatches" value="2" />
-			<param name="partial" value="0" />
-            <output name="output" file="fastx_barcode_splitter1.out">
-                <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
-                <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
-                <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
-                <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
-                <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
-            </output>
-		</test>
-	</tests>
+  <tests>
+    <test>
+      <!-- Split a FASTQ file -->
+      <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
+      <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
+      <param name="barcodeLocation" value="bol" />
+      <param name="mismatches" value="2" />
+      <param name="partial" value="0" />
+      <output name="summary" file="fastx_barcode_splitter1.out" />
+      <collection name="output" type="list">
+        <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
+        <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
+        <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
+        <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
+        <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
+      </collection>
+    </test>
+
+    <test>
+      <!-- Split a FASTQ file, using separate index read -->
+      <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
+      <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
+      <param name="idxfile" value="fastx_barcode_splitter_index.fastq" ftype="fastqsolexa" />
+      <param name="barcodeLocation" value="idxfile" />
+      <param name="mismatches" value="2" />
+      <param name="partial" value="0" />
+      <output name="output" file="fastx_barcode_splitter1.out" />
+      <collection name="split_output" type="list">
+        <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
+        <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
+        <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
+        <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
+        <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
+      </collection>
+    </test>
+  </tests>
 
     <help><![CDATA[
 **What it does**
@@ -92,9 +96,9 @@
 Example::
 
     #This line is a comment (starts with a 'number' sign)
-    BC1	GATCT
-    BC2	ATCGT
-    BC3	GTGAT
+    BC1  GATCT
+    BC2  ATCGT
+    BC3  GTGAT
     BC4 TGTCT
 
 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
@@ -102,20 +106,20 @@
 
 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
 
-The output of this tool is an HTML file, displaying the split counts and the file names.
-In addition, each fastq file produced will be loaded into the galaxy history automatically.
+The output of this tool is a summary tabel displaying the split counts for each barcode identifier.
+In addition, each fastq file produced will be loaded into the galaxy history as part of a collection list.
 ]]>
-	</help>
+  </help>
 
-	<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
-	<citations>
+  <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+  <citations>
         <citation type="bibtex">
-			@misc{gordon_fastx-toolkit_????,
-				title = {{FASTX}-{Toolkit}},
-				url = {http://hannonlab.cshl.edu/fastx_toolkit/index.html},
-				author = {Gordon, Assaf}
-			}
-		</citation>
-	</citations>
+      @misc{gordon_fastx-toolkit_????,
+        title = {{FASTX}-{Toolkit}},
+        url = {http://hannonlab.cshl.edu/fastx_toolkit/index.html},
+        author = {Gordon, Assaf}
+      }
+    </citation>
+  </citations>
 
 </tool>