Mercurial > repos > devteam > fastq_trimmer_by_quality

changeset 3:178d14eb7546 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit 522233252089aa58d367cf136e82a8e52f5eb7df
author devteam
date Thu, 02 Feb 2017 17:03:25 -0500
parents 61b9d9f80662
children 8b85db5a62e6
files fastq_trimmer_by_quality.xml tool_dependencies.xml
diffstat 2 files changed, 13 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_trimmer_by_quality.xml	Fri Dec 18 19:01:05 2015 -0500
+++ b/fastq_trimmer_by_quality.xml	Thu Feb 02 17:03:25 2017 -0500
@@ -1,17 +1,17 @@
-<tool id="fastq_quality_trimmer" name="FASTQ Quality Trimmer" version="1.0.0">
+<tool id="fastq_quality_trimmer" name="FASTQ Quality Trimmer" version="1.0.1">
   <description>by sliding window</description>
   <requirements>
-    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
+    <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
   </requirements>
-  <command interpreter="python">fastq_trimmer_by_quality.py '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s '$window_size' 
-    -t '$step_size' -e '$trim_ends' -a '$aggregation_action' -x '$exclude_count' -c '$score_comparison' -q '$quality_score' 
-    #if $keep_zero_length.value:
+  <command>python '$__tool_directory__/fastq_trimmer_by_quality.py' '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s $window_size
+    -t $step_size -e $trim_ends -a $aggregation_action -x $exclude_count -c '$score_comparison' -q $quality_score
+    #if $keep_zero_length:
         -k
     #end if
   </command>
   <inputs>
     <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ File"/>
-    <param name="keep_zero_length" label="Keep reads with zero length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" selected="False"/>
+    <param name="keep_zero_length" label="Keep reads with zero length" type="boolean" checked="false"/>
     <param name="trim_ends" type="select" label="Trim ends">
       <option value="53" selected="True">5' and 3'</option>
       <option value="5">5' only</option>
@@ -42,13 +42,13 @@
     <param name="quality_score" label="Quality Score" value="0" type="float" />
   </inputs>
   <outputs>
-    <data name="output_file" format="input" />
+    <data name="output_file" format_source="input_file" />
   </outputs>
   <tests>
     <test>
       <!-- Trim until window size 1 >= 20;both ends -->
       <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-      <param name="keep_zero_length" value="exclude_zero_length" />
+      <param name="keep_zero_length" value="false" />
       <param name="trim_ends" value="53"/>
       <param name="window_size" value="1"/>
       <param name="step_size" value="1"/>
@@ -61,7 +61,7 @@
     <test>
       <!-- Trim until window size 1 >= 20; 5' end only -->
       <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-      <param name="keep_zero_length" value="exclude_zero_length" />
+      <param name="keep_zero_length" value="false" />
       <param name="trim_ends" value="5"/>
       <param name="window_size" value="1"/>
       <param name="step_size" value="1"/>
@@ -74,7 +74,7 @@
     <test>
       <!-- Trim until window size 1 >= 20; 3' end only -->
       <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-      <param name="keep_zero_length" value="exclude_zero_length" />
+      <param name="keep_zero_length" value="false" />
       <param name="trim_ends" value="3"/>
       <param name="window_size" value="1"/>
       <param name="step_size" value="1"/>
@@ -87,7 +87,7 @@
     <test>
       <!-- Trim until window size 2 >= 1;both ends, 1 deviant score -->
       <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-      <param name="keep_zero_length" value="exclude_zero_length" />
+      <param name="keep_zero_length" value="false" />
       <param name="trim_ends" value="53"/>
       <param name="window_size" value="2"/>
       <param name="step_size" value="1"/>
@@ -113,7 +113,7 @@
     <test>
       <!-- Trim entire sequences; discard empty reads -->
       <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-      <param name="keep_zero_length"/>
+      <param name="keep_zero_length" value="false" />
       <param name="trim_ends" value="53"/>
       <param name="window_size" value="1"/>
       <param name="step_size" value="1"/>
@@ -127,7 +127,7 @@
   <help>
 **What it does**
 
-This tool allows you to trim the ends of reads based upon the aggregate value of quality scores found within a sliding window; a sliding window of size 1 is equivalent to 'simple' trimming of the ends. 
+This tool allows you to trim the ends of reads based upon the aggregate value of quality scores found within a sliding window; a sliding window of size 1 is equivalent to 'simple' trimming of the ends.
 
 The user specifies the aggregating action (min, max, sum, mean) to perform on the quality score values found within the sliding window to be used with the user defined comparison operation and comparison value.
 
@@ -138,10 +138,6 @@
 .. class:: warningmark
 
 Trimming a color space read will cause any adapter base to be lost.
-
-------
-
-
   </help>
   <citations>
     <citation type="doi">10.1093/bioinformatics/btq281</citation>
--- a/tool_dependencies.xml	Fri Dec 18 19:01:05 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="galaxy_sequence_utils" version="1.0.0">
-      <repository changeset_revision="6334612a010e" name="package_galaxy_utils_1_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>