Mercurial > repos > devteam > fastq_masker_by_quality

diff fastq_masker_by_quality.xml @ 2:eb592e9ec47a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 14:58:34 -0400
parents 9d234265981e
children 9282652e7234
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line diff
--- a/fastq_masker_by_quality.xml	Wed Nov 11 12:41:24 2015 -0500
+++ b/fastq_masker_by_quality.xml	Sat Sep 30 14:58:34 2017 -0400
@@ -1,61 +1,59 @@
-<tool id="fastq_masker_by_quality" name="FASTQ Masker" version="1.0.0">
-  <description>by quality score</description>
-  <requirements>
-    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
-  </requirements>
-  <command interpreter="python">fastq_masker_by_quality.py '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s '${quality_score}' -c '${score_comparison}'
-      #if $mask_type.value == 'lowercase'
-      --lowercase
-      #else
-      -m '${mask_type}'
-      #end if
-  </command>
-  <inputs>
-    <param name="input_file" type="data" format="fastqsanger" label="File to mask" />
-    <param name="mask_type" type="select" label="Mask input with">
-      <option value="N">N's</option>
-      <option value="lowercase">Lowercase</option>
-    </param>
-    <param name="score_comparison" type="select" label="When score is">
-      <option value="le" selected="True">Less than or equal</option>
-      <option value="lt">Less than</option>
-      <option value="eq">Equal to</option>
-      <option value="ne">Not Equal to</option>
-      <option value="ge">Greater than</option>
-      <option value="gt">Greater than or equal</option>
-    </param>
-    <param name="quality_score" type="integer" value="0" label="Quality score"/>
-  </inputs>
-  <outputs>
-    <data name="output_file" format="fastqsanger" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-      <param name="mask_type" value="N" />
-      <param name="score_comparison" value="le" />
-      <param name="quality_score" value="20" />
-      <output name="output_file" file="sanger_full_range_masked_N.fastqsanger" />
-    </test>
-    <test>
-      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-      <param name="mask_type" value="lowercase" />
-      <param name="score_comparison" value="le" />
-      <param name="quality_score" value="20" />
-      <output name="output_file" file="sanger_full_range_masked_lowercase.fastqsanger" />
-    </test>
-  </tests>
-  <help>
+<tool id="fastq_masker_by_quality" name="FASTQ Masker" version="1.1.1">
+    <description>by quality score</description>
+    <requirements>
+        <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
+    </requirements>
+    <command><![CDATA[
+gx-fastq-masker-by-quality '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s ${quality_score} -c ${score_comparison}
+#if $mask_type.value == 'lowercase'
+    --lowercase
+#else
+    -m ${mask_type}
+#end if
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="File to mask" />
+        <param name="mask_type" type="select" label="Mask input with">
+            <option value="N">N's</option>
+            <option value="lowercase">Lowercase</option>
+        </param>
+        <param name="score_comparison" type="select" label="When score is">
+            <option value="le" selected="true">Less than or equal</option>
+            <option value="lt">Less than</option>
+            <option value="eq">Equal to</option>
+            <option value="ne">Not Equal to</option>
+            <option value="ge">Greater than</option>
+            <option value="gt">Greater than or equal</option>
+        </param>
+        <param name="quality_score" type="integer" value="0" label="Quality score"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format_source="input_file" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
+            <param name="mask_type" value="N" />
+            <param name="score_comparison" value="le" />
+            <param name="quality_score" value="20" />
+            <output name="output_file" file="sanger_full_range_masked_N.fastqsanger" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
+            <param name="mask_type" value="lowercase" />
+            <param name="score_comparison" value="le" />
+            <param name="quality_score" value="20" />
+            <output name="output_file" file="sanger_full_range_masked_lowercase.fastqsanger" ftype="fastqsanger" />
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 This tool allows masking base characters in FASTQ format files dependent upon user specified quality score value and comparison method.
 
 This tool is not available for use on color space (csSanger) formats.
-
-  </help>
-  
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq281</citation>
-  </citations>
-  
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btq281</citation>
+    </citations>
 </tool>