Mercurial > repos > fubar > mashmap
changeset 6:27df186d5446 draft
planemo upload
| author | fubar |
|---|---|
| date | Sat, 24 Feb 2024 04:11:27 +0000 |
| parents | 10e4181a6443 |
| children | 53f601fb8664 |
| files | mashmap.xml |
| diffstat | 1 files changed, 7 insertions(+), 6 deletions(-) [+] |
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--- a/mashmap.xml Fri Feb 23 09:59:25 2024 +0000 +++ b/mashmap.xml Sat Feb 24 04:11:27 2024 +0000 @@ -1,6 +1,6 @@ <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 toolfactory@galaxy.org at 23/02/2024 20:50:55 using the Galaxy Tool Factory.--> + <!--Created by toolfactory@galaxy.org 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> @@ -11,9 +11,9 @@ <configfile name="runme"><![CDATA[#if len($reflist) > 1: #for i, mash in enumerate($reflist): #if i == 0: - echo $mash > 'reflist' && + echo '$mash' > 'reflist' && #else: - echo $mash >> 'reflist' && + echo '$mash' >> 'reflist' && #end if #end for #end if @@ -22,11 +22,11 @@ -J '$sketchSize' \ #end if #if len($reflist) == 1: - -r $reflist -q '$query' && + -r '$reflist' -q '$query' && #else --rl 'reflist' -q '$query' && #end if -cp 'mashmap.out' $mashout]]></configfile> +cp 'mashmap.out' '$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"/> @@ -70,7 +70,8 @@ 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. + 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: