Mercurial > repos > bgruening > repeat_masker

--- a/repeatmasker.xml.orig	Mon Apr 24 10:29:31 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,260 +0,0 @@
-<<<<<<< HEAD
-<tool id="repeatmasker_wrapper" name="RepeatMasker" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
-    <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro='xrefs'/>
-    <expand macro='edam_ontology' />
-    <expand macro='requirements' />
-    <version_command>repeatmasker --version</version_command>
-    <command detect_errors="exit_code"><![CDATA[
-=======
-<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.1.1" profile="17.01">
-  <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
-  <xrefs>
-      <xref type="bio.tools">RepeatMasker</xref>
-  </xrefs>
-  <requirements>
-    <requirement type="package" version="4.1.1">repeatmasker</requirement>
-  </requirements>
-
-  <command detect_errors="exit_code"><![CDATA[
->>>>>>> c895e2728 (Update repeatmasker.xml)
-    RM_PATH=\$(which RepeatMasker) &&
-    if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&
-
-    RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries &&
-    #if $repeat_source.source_type == "dfam_up":
-      mkdir lib/ &&
-      ln -s '${repeat_source.dfam_lib}' lib/RepeatMaskerLib.h5 &&
-      RM_LIB_PATH=\$(pwd)/lib &&
-    #end if
-
-    ln -s '${input_fasta}' rm_input.fasta &&
-
-    RepeatMasker -dir \$(pwd)
-    -libdir \$RM_LIB_PATH
-    #if $repeat_source.source_type == "library":
-      -lib '${repeat_source.repeat_lib}'
-      -cutoff '${repeat_source.cutoff}'
-    #else if $repeat_source.source_type == "dfam":
-      #if $repeat_source.species_source.species_from_list == 'yes':
-        -species $repeat_source.species_source.species_list
-      #else
-        -species '${repeat_source.species_source.species_name}'
-      #end if
-    #else if $repeat_source.source_type == "dfam_up":
-        -species '${repeat_source.species_name}'
-    #end if
-    -parallel \${GALAXY_SLOTS:-1}
-    ${gff}
-    ${excln}
-    ${advanced.is_only}
-    ${advanced.is_clip}
-    ${advanced.no_is}
-    ${advanced.rodspec}
-    ${advanced.primspec}
-    ${advanced.nolow}
-    ${advanced.noint}
-    ${advanced.norna}
-    ${advanced.alu}
-    ${advanced.div}
-    ${advanced.search_speed}
-    -frag ${advanced.frag}
-    ## -maxsize ${advanced.maxsize}
-    #if str($advanced.gc):
-      -gc ${advanced.gc}
-    #end if
-    ${advanced.gccalc}
-    ${advanced.nocut}
-    ${advanced.keep_alignments}
-    ${advanced.invert_alignments}
-    ${advanced.xout}
-    ${advanced.xsmall}
-    ${advanced.poly}
-    rm_input.fasta &&
-    #if $advanced.is_only != '-is_only':
-      mv rm_input.fasta.masked '${output_masked_genome}' &&
-      sed -E 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g ;  1,2c SW score\t% div.\t% del.\t% ins.\tquery sequence\tpos in  query: begin\tend\t(left)\trepeat\tclass/family\tpos in repeat: begin\tend\t(left)\tID' rm_input.fasta.out >'${output_log}' &&
-      mv rm_input.fasta.tbl '${output_table}' &&
-      #if $gff == '-gff':
-        mv rm_input.fasta.out.gff '${output_gff}' &&
-      #end if
-      #if $advanced.keep_alignments == '-ali':
-        mv rm_input.fasta.align '${output_alignment}' &&
-      #end if
-      #if $advanced.poly == '-poly':
-        sed -E 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g' rm_input.fasta.polyout >'${output_polymorphic}' &&
-      #end if
-    #end if
-    if [ -f 'rm_input.fasta.cat.gz' ]; then
-      zcat 'rm_input.fasta.cat.gz' > '${output_repeat_catalog}';
-    else
-      mv rm_input.fasta.cat '${output_repeat_catalog}';
-    fi
-    ]]>
-  </command>
-
-  <inputs>
-    <param name="input_fasta" type="data" format="fasta" label="Genomic DNA" />
-    <conditional name="repeat_source">
-      <param label="Repeat library source" name="source_type" type="select" help="To use RepBase, choose 'Custom library of repeats' and select a fasta version of this non-free database.">
-        <option selected="true" value="dfam">DFam (curated only, bundled with RepeatMasker)</option>
-        <option value="dfam_up">DFam (full/specific version)</option>
-        <option value="library">Custom library of repeats</option>
-      </param>
-      <when value="dfam">
-        <conditional name="species_source">
-          <param label="Select species name from a list?" name="species_from_list" type="select">
-            <option value="yes" selected="true">Yes</option>
-            <option value="no">No</option>
-          </param>
-          <when value="yes">
-            <param name="species_list" type="select" label="Species">
-              <option value="human" selected="true">Human (Homo sapiens)</option>
-              <option value="rodent">Rodent (Order Rodentia)</option>
-              <option value="mouse">Mouse (Mus musculus)</option>
-              <option value="rattus">Rat (Rattus sp.)</option>
-              <option value="danio">Danio (zebra fish)</option>
-              <option value="drosophila">Fruit fly (Drosophila melanogaster)</option>
-              <option value="elegans">Caenorhabditis elegans (nematode)</option>
-            </param>
-          </when>
-          <when value="no">
-            <param name="species_name" type="text" value="human" label="Repeat source species" help="Source species (or clade name) used to select repeats from DFam" />
-          </when>
-        </conditional>
-      </when>
-      <when value="dfam_up">
-          <param name="dfam_lib" type="data" format="h5" label="DFam library" help="The full DFam library can be downloaded from https://www.dfam.org/releases/current/families/Dfam.h5.gz" />
-          <param name="species_name" type="text" value="human" label="Repeat source species" help="Source species (or clade name) used to select repeats from DFam" />
-      </when>
-      <when value="library">
-        <param name="repeat_lib" type="data" format="fasta" label="Custom library of repeats" />
-        <param name="cutoff" type="integer" argument="-cutoff" value="225" label="Cutoff score for masking repeats" />
-      </when>
-    </conditional>
-    <param type="boolean" argument="-gff" truevalue="-gff" falsevalue="" label="Output annotation of repeats in GFF format" checked="false" />
-    <param argument="-excln" type="boolean" truevalue="-excln" falsevalue="" label="Ignore stretches of Ns when computing statistics" checked="true" help="Scaffolds are sometimes joined with stretches of 25 or more Ns. This option ignores them when calculating repeat statistics" />
-    <section name="advanced" title="Advanced options" expanded="false">
-      <param argument="-is_only" type="boolean" truevalue="-is_only" falsevalue="" checked="false" label="Only clip E coli insertion elements" />
-      <param argument="-is_clip" type="boolean" truevalue="-is_clip" falsevalue="" checked="false" label="Clip IS elements before analysis" help="Normally RepeatMasker will report on IS element, with this option selected it will clip them before analysis" />
-      <param argument="-no_is" type="boolean" truevalue="-no_is" falsevalue="" checked="false" label="Skip bacterial insertion element check" />
-      <param argument="-rodspec" type="boolean" truevalue="-rodspec" falsevalue="" checked="false" label="Only check for rodent specific repeats" help="If this option is select a check for rodent specific repeats is done instead of a full RepeatMasker run" />
-      <param argument="-primspec" type="boolean" truevalue="-primspec" falsevalue="" checked="false" label="Only check for primate specific repeats" help="If this option is select a check for primate specific repeats is done instead of a full RepeatMasker run" />
-      <param argument="-nolow" type="boolean" truevalue="-nolow" falsevalue="" checked="false" label="No low complexity masking" help="Skip masking of simple tandem repeats and low complexity regions." />
-      <param argument="-noint" type="boolean" truevalue="-noint" falsevalue="" checked="false" label="No interspersed repeat masking" help="Only mask simple repeats, skip masking of interspersed repeats." />
-      <param argument="-norna" type="boolean" truevalue="-norna" falsevalue="" checked="false" label="No repeat-like-RNA masking" help="Skip masking of small pol III transcribed RNA (these are masked by default because they resemble SINEs)" />
-      <param argument="-alu" type="boolean" truevalue="-alu" falsevalue="" checked="false" label="Limit masking to (primate) Alu repeats" />
-      <param argument="-div" type="boolean" truevalue="-div" falsevalue="" checked="false" label="Limit masking to less diverged (younger) repeats" />
-      <param type="select" name="search_speed" label="Search speed vs sensitiviy trade-off">
-        <option value="">Default</option>
-        <option value="-q">Quick (5-10% less sensitive, 3-4 times speedup)</option>
-        <option value="-qq">Rush (10% less sensitive)</option>
-        <option value="-s">Slow (0-5% more sensitive, 2.5 times slowdown)</option>
-      </param>
-      <param type="integer" argument="-frag" value="40000" label="Maximum contiguous sequence searched" help="Maximum length of sequencing that is search without fragmenting" />
-      <!-- -maxsize option is in the help, but not in the code of repeatmasker-->
-      <!--param type="integer" argument="-maxsize" value="4000000" label="Maximum length for IS or repeat clipped sequences" /-->
-      <param type="integer" argument="-gc" optional="true" label="Select matrices for this GC%" help="Valid values are a percentage or -1 to choose the default" />
-      <param type="boolean" argument="-gccalc" truevalue="-gcccalc" falsevalue="" checked="false" label="Calculate GC % for all sequences" help="By default RepeatMasker skips calculating GC % for small sequences" />
-      <param type="boolean" argument="-nocut" truevalue="-nocut" falsevalue="" checked="false" label="Skips cutting of repeats" />
-      <param name="xout" type="boolean" argument="-x" truevalue="-x" falsevalue="" checked="false" label="Mask with X instead of N characters" />
-      <param name="keep_alignments" type="boolean" argument="-ali" truevalue="-ali" falsevalue="" checked="false" label="Output alignments file" />
-      <param name="invert_alignments" type="boolean" argument="-inv" truevalue="-inv" falsevalue="" checked="false" label="Invert alignments in alignment file" help="Show alignments in the orientation of the repeat sequence, not the query sequence" />
-      <param type="boolean" argument="-xsmall" truevalue="-xsmall" falsevalue="" checked="false" label="Output repetitive regions as lowercase, non-repetitive regions as uppercase" />
-      <param type="boolean" argument="-poly" truevalue="-poly" falsevalue="" checked="false" label="Output list of potentially polymorphic microsatellites" />
-    </section>
-  </inputs>
-  <outputs>
-    <data name="output_masked_genome" format="fasta" label="RepeatMasker masked sequence on ${on_string}">
-      <filter>not advanced['is_only']</filter>
-    </data>
-    <data name="output_log" format="tabular" label="RepeatMasker output log on ${on_string}">
-      <filter>not advanced['is_only']</filter>
-    </data>
-    <data name="output_table" format="txt" label="RepeatMasker repeat statistics on ${on_string}">
-      <filter>not advanced['is_only']</filter>
-    </data>
-    <data name="output_repeat_catalog" format="txt" label="RepeatMasker repeat catalogue on ${on_string}" />
-    <data name="output_alignment" format="txt" label="RepeatMasker alignment on ${on_string}">
-      <filter>not advanced['is_only'] and advanced['keep_alignments']</filter>
-    </data>
-    <data name="output_polymorphic" format="tabular" label="RepeatMasker possible polymorphic repeats on ${on_string}">
-      <filter>not advanced['is_only'] and advanced['poly']</filter>
-    </data>
-    <data name="output_gff" format="gff" label="RepeatMasker repeat annotation on ${on_string}">
-      <filter>not advanced['is_only'] and gff is True</filter>
-    </data>
-  </outputs>
-  <tests>
-    <test expect_num_outputs="4">
-      <param name="input_fasta" value="small.fasta" ftype="fasta" />
-      <param name="source_type" value="library" />
-      <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />
-      <output name="output_masked_genome" file="small.fasta.masked" />
-      <output name="output_table" file="small.fasta.stats" lines_diff="6" />
-      <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
-      <output name="output_log" file="small.fasta.log" lines_diff="2"/>
-    </test>
-    <test expect_num_outputs="7">
-      <param name="input_fasta" value="small.fasta" ftype="fasta" />
-      <param name="source_type" value="library" />
-      <param name="gff" value="-gff" />
-      <param name="keep_alignments" value="-ali" />
-      <param name="poly" value="-poly" />
-      <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />
-      <output name="output_masked_genome" file="small.fasta.masked" />
-      <output name="output_table" file="small.fasta.stats" lines_diff="6" />
-      <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
-      <output name="output_log" file="small.fasta.log" lines_diff="2"/>
-      <output name="output_alignment" file="small.fasta.align" />
-      <output name="output_polymorphic" file="small.fasta.poly" />
-      <output name="output_gff" file="small.fasta.gff" lines_diff="4" />
-    </test>
-    <test expect_num_outputs="4">
-      <param name="input_fasta" value="small.fasta" ftype="fasta" />
-      <param name="source_type" value="dfam" />
-      <param name="species_list" value="human" />
-      <output name="output_masked_genome" file="small_dfam.fasta.masked" />
-      <output name="output_table" file="small_dfam.fasta.stats" lines_diff="2" />
-      <output name="output_repeat_catalog" file="small_dfam.fasta.cat" lines_diff="2" />
-      <output name="output_log" file="small_dfam.fasta.log" lines_diff="2"/>
-    </test>
-    <test expect_num_outputs="4">
-      <param name="input_fasta" value="small.fasta" ftype="fasta" />
-      <param name="source_type" value="dfam_up" />
-      <param name="dfam_lib" value="Dfam_partial_test.h5" ftype="h5" />
-      <param name="species_name" value="rodent" />
-      <output name="output_masked_genome" file="small_dfam_up.fasta.masked" />
-      <output name="output_table" file="small_dfam_up.fasta.stats" lines_diff="2" />
-      <output name="output_repeat_catalog" file="small_dfam_up.fasta.cat" lines_diff="2" />
-      <output name="output_log" file="small_dfam_up.fasta.log" lines_diff="2"/>
-    </test>
-    <test expect_num_outputs="4">
-      <param name="input_fasta" value="small.fasta" ftype="fasta" />
-      <param name="source_type" value="dfam" />
-      <param name="species_list" value="rattus" />
-      <output name="output_masked_genome" file="small_dfam_rattus.fasta.masked" />
-      <output name="output_table" file="small_dfam_rattus.fasta.stats" lines_diff="2" />
-      <output name="output_repeat_catalog" file="small_dfam_rattus.fasta.cat" lines_diff="2" />
-      <output name="output_log" file="small_dfam_rattus.fasta.log" lines_diff="2"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-RepeatMasker is a program that screens DNA for interspersed repeats and low
-complexity DNA sequences. The database of repeats to screen for can be
-provided as a FASTA file or downloaded from RepBase_. If the RepBase option is
-chosen the RepBaseRepeatMaskerEdition file should be downloaded and
-unpacked, and the enclosed EMBL format file ('RMRBSeqs.embl') should
-be uploaded to Galaxy for use with this tool.
-
-Further documentation is available on the RepeatMasker homepage_.
-
-.. _RepBase: http://www.girinst.org/repbase/
-.. _homepage: http://www.repeatmasker.org/webrepeatmaskerhelp.html
-    ]]>
-  </help>
-  <expand macro="citations" />
-</tool>