comparison picard_NormalizeFasta.xml @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8

32:f9242e01365a

<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>normalize fasta datasets</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">1</token>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@

    ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
    #import re
    #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
    ln -f -s '$inputFile' '$escaped_element_identifier'.fa &&
    picard
    NormalizeFasta

    INPUT='$escaped_element_identifier'.fa
    OUTPUT="${outFile}"
    LINE_LENGTH="${line_length}"
    TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"

    QUIET=true
    VERBOSITY=ERROR

  ]]></command>
  <inputs>
    <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" />
    <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
    <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
  </inputs>

  <outputs>
    <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
  </outputs>

  <tests>
    <test>
      <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
      <param name="line_length" value="40"/>
      <param name="truncate_sequence_names_at_whitespaces" value="False"/>
      <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
    </test>
  </tests>


  <help>

**Purpose**

Takes any dataset that conforms to the fasta format and normalizes it so that all lines of sequence except the last line per named sequence are of the same length.

                                Truncate sequence names at first whitespace.  Default value: false. Possible values: {true, false}

@more_info@

  </help>
  <expand macro="citations" />
</tool>

33:3f254c5ced1d

<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>normalize fasta datasets</description>
    <macros>
        <import>picard_macros.xml</import>
        <token name="@WRAPPER_VERSION@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
    @java_options@

    ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
    #import re
    #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
    ln -sf '$inputFile' '$escaped_element_identifier'.fa &&
    
    picard NormalizeFasta

    --INPUT '$escaped_element_identifier'.fa
    --OUTPUT '${outFile}'
    --LINE_LENGTH '${line_length}'
    --TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE '${truncate_sequence_names_at_whitespaces}'

    --QUIET true
    --VERBOSITY ERROR

  ]]></command>
    <inputs>
        <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset"/>
        <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
        <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
    </inputs>
    <outputs>
        <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
    </outputs>
    <tests>
        <test>
            <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
            <param name="line_length" value="40"/>
            <param name="truncate_sequence_names_at_whitespaces" value="False"/>
            <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
        </test>
    </tests>
    <help>

**Purpose**

Takes any dataset that conforms to the fasta format and normalizes it so that all lines of sequence except the last line per named sequence are of the same length.

                                Truncate sequence names at first whitespace.  Default value: false. Possible values: {true, false}

@more_info@

  </help>
    <expand macro="citations"/>
</tool>