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comparison fastq_trimmer.xml @ 2:fdff6f6a8763 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author devteam
date Fri, 18 Dec 2015 19:31:05 -0500
parents 3be753901f6e
children b849e7c23b43
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1:3be753901f6e 2:fdff6f6a8763
1 <tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.0.0"> 1 <tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.0.1">
2 <description>by column</description> 2 <description>by column</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> 4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">fastq_trimmer.py '$input_file' '$output_file' '${offset_type['left_column_offset']}' '${offset_type['right_column_offset']}' '${offset_type['base_offset_type']}' '${input_file.extension[len( 'fastq' ):]}' '$keep_zero_length'</command> 6 <command interpreter="python">fastq_trimmer.py '$input_file' '$output_file' '${offset_type['left_column_offset']}' '${offset_type['right_column_offset']}' '${offset_type['base_offset_type']}' '${input_file.extension[len( 'fastq' ):]}' '$keep_zero_length'</command>
14 <when value="offsets_absolute"> 14 <when value="offsets_absolute">
15 <param name="left_column_offset" label="Offset from 5' end" value="0" type="integer" help="Values start at 0, increasing from the left"> 15 <param name="left_column_offset" label="Offset from 5' end" value="0" type="integer" help="Values start at 0, increasing from the left">
16 <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> 16 <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/>
17 <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> 17 <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
18 </param> 18 </param>
19 <param name="right_column_offset" label="Offset from 3' end" value="0" type="integer" help="Values start at 0, increasing from the right"> 19 <param name="right_column_offset" label="Offset from 3' end" value="0" type="integer" help="Values start at 0, increasing from the right; use a negative value to remove everything to the right of the absolute value of the position">
20 <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/>
21 <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> 20 <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
22 </param> 21 </param>
23 </when> 22 </when>
24 <when value="offsets_percent"> 23 <when value="offsets_percent">
25 <param name="left_column_offset" label="Offset from 5' end" value="0" type="float"> 24 <param name="left_column_offset" label="Offset from 5' end" value="0" type="float">