comparison mashmap.xml @ 10:08a74c1a4562 draft default tip

planemo upload

9:dc53eb4354a6

<tool name="mashmap" id="mashmap" version="1.19.2" profile="22.05">
  <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
  <!--Created by [e-mail] at 24/02/2024 19:18:09 using the Galaxy Tool Factory.-->
  <description>Fast local alignment boundaries</description>
  <requirements>
    <requirement version="3.1.3" type="package">mashmap</requirement>
    <requirement version="1.19.2" type="package">samtools</requirement>
  </requirements>

samtools faidx 'query' &&
mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \
#if int($sketchSize) > 0:
-J '$sketchSize' \
#end if
#if len($reflist) == 1:
 -r '$reflist' -q 'query' && 
#else
--rl 'reflist' -q 'query' && 
#end if

    <param name="query" type="data" optional="false" label="Query sequences (as fasta) to mash against the references supplied below" help="" format="fasta" multiple="false"/>
    <param name="reflist" type="data" optional="false" label="Reference or references to mash the query sequences on" help="Choose one or more reference sequences to mash the query sequences against." format="fasta" multiple="true"/>
    <param name="perc_identity" type="float" value="85.0" label="Identity threshold" help="By default, it is set to 85, implying mappings with 85 or more identity should be reported. For example, it can be set to 80to account for more noisy long-read datasets or 95 for mapping human genome assembly to human reference."/>
    <param name="seqLength" type="integer" value="5000" label="Minimum segment length" help="Default is 5,000 bp. Sequences below this length are ignored. Mashmap provides guarantees on reporting local alignments of length twice this value."/>
    <param name="sketchSize" type="integer" value="0" label="Sketch size - leave 0 for automatic setting based" help="This parameter sets the seed density of the winnowing scheme, gauranteeing that the minhash will be calculated from a sample of sketchSize k-mers for each segment. It is set automatically based on --pi but can be manually set as well."/>
    <param name="dense" type="select" label="Dense sketching" help="This flag will increase the seed density substantially, resulting in a density of roughly 0.02 * (1 + (1 - pi) / .05) where pi is the perc_identity threshold. This leads to longer runtimes and higher RAM usage, but significantly more accurate estimates of ANI.">
      <option value="">No dense sketching</option>
      <option value="--dense">Dense sketching</option>
    </param>
    <param name="filtermode" type="select" label="Filter mode" help="Mashmap implements a plane-sweep based algorithm to perform the alignment filtering. Similar to delta-filter in nucmer, different filtering options are provided that are suitable for long read or assembly mapping. Option -f map is suitable for reporting the best mappings for long reads, whereas -f one-to-one is suitable for reporting orthologous mappings among all computed assembly to genome mappings.">
      <option value="map">map - best mapping for long reads</option>
      <option value="one-to-one">one-to-one - best for mapping orthologous reads</option>
      <option value="none">None</option>
    </param>

      <param name="query" value="query_sample"/>
      <param name="reflist" value="reflist_sample"/>
      <param name="perc_identity" value="85.0"/>
      <param name="seqLength" value="5000"/>
      <param name="sketchSize" value="0"/>
      <param name="dense" value=""/>
      <param name="filtermode" value="map"/>
    </test>
  </tests>
  <help><![CDATA[
 *MashMap* implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences. It can be useful for mapping genome assembly or long reads (PacBio/ONT) to reference genome(s). Given a minimum alignment length and an identity threshold for the desired local alignments, 

10:08a74c1a4562

<tool name="mashmap" id="mashmap" version="1.19.2" profile="22.05">
  <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
  <!--Created by [e-mail] at 24/02/2024 19:28:59 using the Galaxy Tool Factory.-->
  <description>Fast local alignment boundaries</description>
  <requirements>
    <requirement version="3.1.3" type="package">mashmap</requirement>
    <requirement version="1.19.2" type="package">samtools</requirement>
  </requirements>

samtools faidx 'query' &&
mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \
#if int($sketchSize) > 0:
-J '$sketchSize' \
#end if
#if $dense:
--dense \
#end if
#if len($reflist) == 1:
 -r '$reflist' -q 'query' && 
#else
--rl 'reflist' -q 'query' && 
#end if

    <param name="query" type="data" optional="false" label="Query sequences (as fasta) to mash against the references supplied below" help="" format="fasta" multiple="false"/>
    <param name="reflist" type="data" optional="false" label="Reference or references to mash the query sequences on" help="Choose one or more reference sequences to mash the query sequences against." format="fasta" multiple="true"/>
    <param name="perc_identity" type="float" value="85.0" label="Identity threshold" help="By default, it is set to 85, implying mappings with 85 or more identity should be reported. For example, it can be set to 80to account for more noisy long-read datasets or 95 for mapping human genome assembly to human reference."/>
    <param name="seqLength" type="integer" value="5000" label="Minimum segment length" help="Default is 5,000 bp. Sequences below this length are ignored. Mashmap provides guarantees on reporting local alignments of length twice this value."/>
    <param name="sketchSize" type="integer" value="0" label="Sketch size - leave 0 for automatic setting based" help="This parameter sets the seed density of the winnowing scheme, gauranteeing that the minhash will be calculated from a sample of sketchSize k-mers for each segment. It is set automatically based on --pi but can be manually set as well."/>
    <param name="dense" type="boolean" value="false" label="Dense sketching" help="This flag will increase the seed density substantially, resulting in a density of roughly 0.02 * (1 + (1 - pi) / .05) where pi is the perc_identity threshold. This leads to longer runtimes and higher RAM usage, but significantly more accurate estimates of ANI." checked="false" truevalue="--dense" falsevalue=""/>
    <param name="filtermode" type="select" label="Filter mode" help="Mashmap implements a plane-sweep based algorithm to perform the alignment filtering. Similar to delta-filter in nucmer, different filtering options are provided that are suitable for long read or assembly mapping. Option -f map is suitable for reporting the best mappings for long reads, whereas -f one-to-one is suitable for reporting orthologous mappings among all computed assembly to genome mappings.">
      <option value="map">map - best mapping for long reads</option>
      <option value="one-to-one">one-to-one - best for mapping orthologous reads</option>
      <option value="none">None</option>
    </param>

      <param name="query" value="query_sample"/>
      <param name="reflist" value="reflist_sample"/>
      <param name="perc_identity" value="85.0"/>
      <param name="seqLength" value="5000"/>
      <param name="sketchSize" value="0"/>
      <param name="dense" value="false"/>
      <param name="filtermode" value="map"/>
    </test>
  </tests>
  <help><![CDATA[
 *MashMap* implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences. It can be useful for mapping genome assembly or long reads (PacBio/ONT) to reference genome(s). Given a minimum alignment length and an identity threshold for the desired local alignments,