Mercurial > repos > fubar > mashmap
diff mashmap.xml @ 7:53f601fb8664 draft
planemo upload
| author | fubar |
|---|---|
| date | Sat, 24 Feb 2024 04:32:36 +0000 |
| parents | 27df186d5446 |
| children | 9ba0184870ef |
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--- a/mashmap.xml Sat Feb 24 04:11:27 2024 +0000 +++ b/mashmap.xml Sat Feb 24 04:32:36 2024 +0000 @@ -1,11 +1,12 @@ -<tool name="mashmap" id="mashmap" version="3.1.3" profile="22.05"> +<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 toolfactory@galaxy.org at 23/02/2024 21:34:16 using the Galaxy Tool Factory.--> + <!--Created by toolfactory@galaxy.org at 24/02/2024 15:30:44 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> - <version_command><![CDATA[echo "3.1.3"]]></version_command> + <version_command><![CDATA[echo "1.19.2"]]></version_command> <command><![CDATA[bash '$runme']]></command> <configfiles> <configfile name="runme"><![CDATA[#if len($reflist) > 1: @@ -17,6 +18,7 @@ #end if #end for #end if +samtools faidx '$query' && mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \ #if int($sketchSize) > 0: -J '$sketchSize' \ @@ -70,8 +72,7 @@ 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. + 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: