Mercurial > repos > fubar > mashmap
changeset 9:dc53eb4354a6 draft
planemo upload
| author | fubar |
|---|---|
| date | Sat, 24 Feb 2024 08:20:07 +0000 |
| parents | 9ba0184870ef |
| children | 08a74c1a4562 |
| files | mashmap.bash.txt mashmap.xml |
| diffstat | 2 files changed, 27 insertions(+), 5 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mashmap.bash.txt Sat Feb 24 08:20:07 2024 +0000 @@ -0,0 +1,21 @@ +ln -s '$query' 'query' && +#if len($reflist) > 1: +#for i, mash in enumerate($reflist): + #if i == 0: + echo '$mash' > 'reflist' && + #else: + echo '$mash' >> 'reflist' && + #end if +#end for +#end if +samtools faidx 'query' && +mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \ +#if int($sketchSize) > 0: +-J '$sketchSize' \ +#end if +#if len($reflist) == 1: + -r '$reflist' -q 'query' && +#else +--rl 'reflist' -q 'query' && +#end if +cp 'mashmap.out' '$mashout'
--- a/mashmap.xml Sat Feb 24 06:58:16 2024 +0000 +++ b/mashmap.xml Sat Feb 24 08:20:07 2024 +0000 @@ -1,6 +1,6 @@ <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 24/02/2024 15:58:22 using the Galaxy Tool Factory.--> + <!--Created by toolfactory@galaxy.org 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> @@ -9,7 +9,8 @@ <version_command><![CDATA[echo "1.19.2"]]></version_command> <command><![CDATA[bash '$runme']]></command> <configfiles> - <configfile name="runme"><![CDATA[#if len($reflist) > 1: + <configfile name="runme"><![CDATA[ln -s '$query' 'query' && +#if len($reflist) > 1: #for i, mash in enumerate($reflist): #if i == 0: echo '$mash' > 'reflist' && @@ -18,15 +19,15 @@ #end if #end for #end if -samtools faidx '$query' && +samtools faidx 'query' && mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \ #if int($sketchSize) > 0: -J '$sketchSize' \ #end if #if len($reflist) == 1: - -r '$reflist' -q '$query' && + -r '$reflist' -q 'query' && #else ---rl 'reflist' -q '$query' && +--rl 'reflist' -q 'query' && #end if cp 'mashmap.out' '$mashout']]></configfile> </configfiles>