comparison fastq_manipulation.xml @ 2:16d28d67ebeb draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit de7140295cce07e1bc1697e51dab4271c8d7a8a6

1:b50aeae8bcaa

<tool id="fastq_manipulation" name="Manipulate FASTQ" version="1.0.1">
  <options sanitize="False" /> <!-- This tool uses a file to rely all parameter information (actually a dynamically generated python module), we can safely not sanitize any parameters -->
  <requirements>
    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
  </requirements>
  <description>reads on various attributes</description>

                  <when value="offsets_absolute">
                    <param name="left_column_offset" label="Offset from 5' end" value="0" type="integer" help="Values start at 0, increasing from the left">
                      <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/>
                      <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
                    </param>
                    <param name="right_column_offset" label="Offset from 3' end" value="0" type="integer" help="Values start at 0, increasing from the right">
                      <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/>
                      <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
                    </param>
                  </when>
                  <when value="offsets_percent">
                    <param name="left_column_offset" label="Offset from 5' end" value="0" type="float">

    right_column_offset = int( round( float( ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] } ) / 100.0 * float( len( new_read ) ) ) )
                #else
    left_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['left_column_offset'] }
    right_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] }
                #end if
    if right_column_offset > 0:
        right_column_offset = -right_column_offset
    else:
        right_column_offset = None
    new_read = new_read.slice( left_column_offset, right_column_offset )
    if not ( ${str( manipulate_block['manipulation_type']['manipulation']['keep_zero_length'] ) == 'keep_zero_length'} or len( new_read ) ):

2:16d28d67ebeb

<tool id="fastq_manipulation" name="Manipulate FASTQ" version="1.0.2">
  <options sanitize="False" /> <!-- This tool uses a file to rely all parameter information (actually a dynamically generated python module), we can safely not sanitize any parameters -->
  <requirements>
    <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
  </requirements>
  <description>reads on various attributes</description>

                  <when value="offsets_absolute">
                    <param name="left_column_offset" label="Offset from 5' end" value="0" type="integer" help="Values start at 0, increasing from the left">
                      <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/>
                      <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
                    </param>
                    <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">
                      <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
                    </param>
                  </when>
                  <when value="offsets_percent">
                    <param name="left_column_offset" label="Offset from 5' end" value="0" type="float">

    right_column_offset = int( round( float( ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] } ) / 100.0 * float( len( new_read ) ) ) )
                #else
    left_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['left_column_offset'] }
    right_column_offset = ${ manipulate_block['manipulation_type']['manipulation']['offset_type']['right_column_offset'] }
                #end if
    if right_column_offset != 0:
        right_column_offset = -right_column_offset
    else:
        right_column_offset = None
    new_read = new_read.slice( left_column_offset, right_column_offset )
    if not ( ${str( manipulate_block['manipulation_type']['manipulation']['keep_zero_length'] ) == 'keep_zero_length'} or len( new_read ) ):