comparison microsatbed.xml @ 9:57867d1931d6 draft

planemo upload for repository https://github.com/fubar2/microsatbed commit 6e9d6a1dd5b8615dfa80b1b239e22b266c00a6dd

8:01c16e8fbc91

<tool id="microsatbedfubar" name="STR to bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
    <description>Short Tandem Repeats to bed features from fasta</description>
    <macros>
        <token name="@TOOL_VERSION@">1.3.2</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PYTHON_VERSION@">3.12.3</token>

        <include path="find_str.py"/>
    </required_files>
    <version_command><![CDATA[python -c "import pytrf; from importlib.metadata import version; print(version('pytrf'))"]]></version_command>
    <command><![CDATA[
  #if $mode_cond.mode == "NATIVE":
    #if $reference_genome.genome_type_select == "history":
      pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.fasta}'
    #else:
      pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.fasta.fields.path}'
    #end if
  #else:
    python '${__tool_directory__}/find_str.py'
    #if str($reference_genome.genome_type_select) == "history":
        --fasta '${reference_genome.fasta}'
    #else:
        --fasta '${reference_genome.fasta.fields.path}'
    #end if
    --bed '$bed'
    #if $mode_cond.mode == "SPECIFIC":
        --specific '$mode_cond.specific'
    #elif $mode_cond.mode == "SPECIFICBW":

            <param name="genome_type_select" type="select" label="Select a source for fasta sequences to be searched for STRs" help="Options are to choose a built-in genome, or choose any history fasta file">
                <option value="indexed">Use a Galaxy server built-in reference genome fasta</option>
                <option value="history" selected="True">Use any fasta file from the current history</option>
            </param>
            <when value="indexed">
                <param name="fasta" type="select" label="Choose a built-in genome" help="If the genome you need is not on the list, upload it and select it as a current history fasta" >
                    <options from_data_table="all_fasta"/>
                </param>
            </when>
            <when value="history">
                <param name="fasta" type="data" format="fasta,fasta.gz" label="Choose a fasta file from the current history" />
            </when>
        </conditional>
        <conditional name="mode_cond">
            <param name="mode" type="select" label="Select patterns by motif length; or provide a specific motif pattern to report?" help="Choose *By length:* or *By pattern:* to configure STR selection mode">
                <option selected="True" value="ALL">By length: Report all motifs of one or more specified lengths (1-6nt) as bed features</option>

        <param name="tetramin" type="integer" min="2" value="2" label="Minimum repeats required for tetramers"/>
        <param name="pentamin" type="integer" min="2" value="2" label="Minimum repeats required for pentamers"/>
        <param name="hexamin" type="integer" min="2" value="2" label="Minimum repeats required for hexamers"/>
    </inputs>
    <outputs>
      <data name="bed" format="bed" label="STR from $fasta.element_identifier">
        <change_format>
            <when input="mode_cond.outformat" value="gff" format="gff"/>
            <when input="mode_cond.outformat" value="csv" format="csv"/>
            <when input="mode_cond.outformat" value="tsv" format="tabular"/>
            <when input="mode_cond.mode" value="ALLBW" format="bigwig"/>

    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="reference_genome">
                <param name="genome_type_select" value="history"/>
                <param name="fasta" value="humsamp.fa"/>
            </conditional>
            <conditional name="mode_cond">
                <param name="mode" value="ALL"/>
                <param name="subset" value="--di,--tri,--tetra,--penta,--hexa"/>
            </conditional>

            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reference_genome">
                <param name="genome_type_select" value="history"/>
                <param name="fasta" value="humsamp.fa"/>
            </conditional>
            <conditional name="mode_cond">
                <param name="mode" value="SPECIFIC"/>
                <param name="specific" value="GC"/>
            </conditional>

            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reference_genome">
                <param name="genome_type_select" value="history"/>
                <param name="fasta" value="mouse.fa"/>
            </conditional>
            <conditional name="mode_cond">
                <param name="mode" value="NATIVE"/>
                <param name="outformat" value="gff"/>
            </conditional>

              </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reference_genome">
                <param name="genome_type_select" value="history"/>
                <param name="fasta" value="humsamp.fa"/>
            </conditional>
            <conditional name="mode_cond">
                <param name="mode" value="SPECIFICBW"/>
                <param name="specific" value="GC"/>
            </conditional>

9:57867d1931d6

<tool id="microsatbed" name="STR to bed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
    <description>Short Tandem Repeats to bed features from fasta</description>
    <macros>
        <token name="@TOOL_VERSION@">1.3.2</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PYTHON_VERSION@">3.12.3</token>

        <include path="find_str.py"/>
    </required_files>
    <version_command><![CDATA[python -c "import pytrf; from importlib.metadata import version; print(version('pytrf'))"]]></version_command>
    <command><![CDATA[
  #if $mode_cond.mode == "NATIVE":
    #if str($reference_genome.genome_type_select) == "history":
      pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.reffa}'
    #else:
      pytrf findstr -f '$mode_cond.outformat' -o '$bed' -r '$monomin' '$dimin' '$trimin' '$tetramin' '$pentamin' '$hexamin' '${reference_genome.reffa.fields.path}'
    #end if
  #else:
    python '${__tool_directory__}/find_str.py'
    #if str($reference_genome.genome_type_select) == "history":
        --fasta '${reference_genome.reffa}'
    #else:
        --fasta '${reference_genome.reffa.fields.path}'
    #end if
    --bed '$bed'
    #if $mode_cond.mode == "SPECIFIC":
        --specific '$mode_cond.specific'
    #elif $mode_cond.mode == "SPECIFICBW":

            <param name="genome_type_select" type="select" label="Select a source for fasta sequences to be searched for STRs" help="Options are to choose a built-in genome, or choose any history fasta file">
                <option value="indexed">Use a Galaxy server built-in reference genome fasta</option>
                <option value="history" selected="True">Use any fasta file from the current history</option>
            </param>
            <when value="indexed">
                <param name="reffa" type="select" label="Choose a built-in genome" help="If the genome you need is not on the list, upload it and select it as a current history fasta" >
                    <options from_data_table="all_fasta"/>
                </param>
            </when>
            <when value="history">
                <param name="reffa" type="data" format="fasta,fasta.gz" label="Choose a fasta file from the current history" />
            </when>
        </conditional>
        <conditional name="mode_cond">
            <param name="mode" type="select" label="Select patterns by motif length; or provide a specific motif pattern to report?" help="Choose *By length:* or *By pattern:* to configure STR selection mode">
                <option selected="True" value="ALL">By length: Report all motifs of one or more specified lengths (1-6nt) as bed features</option>

        <param name="tetramin" type="integer" min="2" value="2" label="Minimum repeats required for tetramers"/>
        <param name="pentamin" type="integer" min="2" value="2" label="Minimum repeats required for pentamers"/>
        <param name="hexamin" type="integer" min="2" value="2" label="Minimum repeats required for hexamers"/>
    </inputs>
    <outputs>
      <data name="bed" format="bed" label="STR">
        <change_format>
            <when input="mode_cond.outformat" value="gff" format="gff"/>
            <when input="mode_cond.outformat" value="csv" format="csv"/>
            <when input="mode_cond.outformat" value="tsv" format="tabular"/>
            <when input="mode_cond.mode" value="ALLBW" format="bigwig"/>

    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="reference_genome">
                <param name="genome_type_select" value="history"/>
                <param name="reffa" value="humsamp.fa"/>
            </conditional>
            <conditional name="mode_cond">
                <param name="mode" value="ALL"/>
                <param name="subset" value="--di,--tri,--tetra,--penta,--hexa"/>
            </conditional>

            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reference_genome">
                <param name="genome_type_select" value="history"/>
                <param name="reffa" value="humsamp.fa"/>
            </conditional>
            <conditional name="mode_cond">
                <param name="mode" value="SPECIFIC"/>
                <param name="specific" value="GC"/>
            </conditional>

            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reference_genome">
                <param name="genome_type_select" value="history"/>
                <param name="reffa" value="mouse.fa"/>
            </conditional>
            <conditional name="mode_cond">
                <param name="mode" value="NATIVE"/>
                <param name="outformat" value="gff"/>
            </conditional>

              </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reference_genome">
                <param name="genome_type_select" value="indexed"/>
                <param name="reffa" value="hgtest"/>
            </conditional>
            <conditional name="mode_cond">
                <param name="mode" value="SPECIFICBW"/>
                <param name="specific" value="GC"/>
            </conditional>