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Galaxy Paired-end Deinterlacer
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GBCS
Galaxy Paired-end Deinterlacer
Commits
8715adec
Commit
8715adec
authored
5 years ago
by
Jelle Scholtalbers
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keep source format; divide slots by 2 for each pigz process
parent
d01b2bc0
Branches
master
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paired-end-deinterlacer.xml
+3
-3
3 additions, 3 deletions
paired-end-deinterlacer.xml
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3 deletions
paired-end-deinterlacer.xml
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3
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8715adec
...
...
@@ -6,7 +6,7 @@
#if not $compress:
zcat $input | paste - - - - - - - - | tee >
(cut -f 1-4 | tr "\t" "\n" > $read1) | cut -f 5-8 | tr "\t" "\n" > $read2
#else:
zcat $input | paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes "\${GALAXY_SLOTS
/2
:-4}" > $read1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes "\${GALAXY_SLOTS
/2
:-4}" > $read2
zcat $input | paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes "\$
((\$
{GALAXY_SLOTS:-4}
/2))
" > $read1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes "\$
((\$
{GALAXY_SLOTS:-4}
/2))
" > $read2
#end if
]]>
</command>
<inputs>
...
...
@@ -15,8 +15,8 @@
</inputs>
<outputs>
<data
name=
"read1"
format
=
"fastq"
label=
"
Read1"
/>
<data
name=
"read2"
format
=
"fastq"
label=
"
Read2"
/>
<data
name=
"read1"
format
_source=
"input"
label=
"${tool.name} on ${on_string}:
Read1"
/>
<data
name=
"read2"
format
_source=
"input"
label=
"${tool.name} on ${on_string}:
Read2"
/>
</outputs>
<tests>
...
...
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