comparison mashmap.xml @ 6:27df186d5446 draft

planemo upload

5:10e4181a6443

<tool name="mashmap" id="mashmap" version="3.1.3" profile="22.05">
  <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
  <!--Created by [e-mail] at 23/02/2024 20:50:55 using the Galaxy Tool Factory.-->
  <description>Fast local alignment boundaries</description>
  <requirements>
    <requirement version="3.1.3" type="package">mashmap</requirement>
  </requirements>
  <version_command><![CDATA[echo "3.1.3"]]></version_command>
  <command><![CDATA[bash '$runme']]></command>
  <configfiles>
    <configfile name="runme"><![CDATA[#if len($reflist) > 1:
#for i, mash in enumerate($reflist):
   #if i == 0:
       echo $mash > 'reflist' &&
   #else:
       echo $mash >> 'reflist' &&
   #end if
#end for
#end if
mashmap --pi '$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
cp 'mashmap.out'  $mashout]]></configfile>
  </configfiles>
  <inputs>
    <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."/>

 
 Map set of query sequences against a reference genome:
 
 mashmap -r reference.fna -q query.fa
 
 The output is space-delimited with each line consisting of query name, length, 0-based start, end, strand, target name, length, start, end and mapping nucleotide identity.
 
 Map set of query seqences against a list of reference genomes:
 
 mashmap --rl referenceList.txt -q query.fa
 

6:27df186d5446

<tool name="mashmap" id="mashmap" version="3.1.3" profile="22.05">
  <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
  <!--Created by [e-mail] at 23/02/2024 21:34:16 using the Galaxy Tool Factory.-->
  <description>Fast local alignment boundaries</description>
  <requirements>
    <requirement version="3.1.3" type="package">mashmap</requirement>
  </requirements>
  <version_command><![CDATA[echo "3.1.3"]]></version_command>
  <command><![CDATA[bash '$runme']]></command>
  <configfiles>
    <configfile name="runme"><![CDATA[#if len($reflist) > 1:
#for i, mash in enumerate($reflist):
   #if i == 0:
       echo '$mash' > 'reflist' &&
   #else:
       echo '$mash' >> 'reflist' &&
   #end if
#end for
#end if
mashmap --pi '$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 '$query' && 
#end if
cp 'mashmap.out'  '$mashout']]></configfile>
  </configfiles>
  <inputs>
    <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."/>

 
 Map set of query sequences against a reference genome:
 
 mashmap -r reference.fna -q query.fa
 
 The output is a paf format file (https://github.com/lh3/miniasm/blob/master/PAF.md).
 Thi is space-delimited with each line consisting of query name, length, 0-based start, end, strand, target name, length, start, end and mapping nucleotide identity.
 
 Map set of query seqences against a list of reference genomes:
 
 mashmap --rl referenceList.txt -q query.fa