Mercurial > repos > chrisw > monorail_test

comparison monorail.xml @ 37:5656cfea6d97 draft

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author chrisw
date Wed, 20 Nov 2019 02:42:57 +0000
parents ad4b5855143b
children 318bff30468a
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36:ad4b5855143b 37:5656cfea6d97
15 <requirement type="package" version="2.9.1">sra-tools</requirement> 15 <requirement type="package" version="2.9.1">sra-tools</requirement>
16 --> 16 -->
17 </requirements> 17 </requirements>
18 <!-- /bin/bash -x monorail.slim.sh ../ath10 4 10 ../ath10/gtf/exons.bed ./tmp2 ../fastqs/SRR8505407_1_100.fastq.gz ../fastqs/SRR8505407_2_100.fastq.gz --> 18 <!-- /bin/bash -x monorail.slim.sh ../ath10 4 10 ../ath10/gtf/exons.bed ./tmp2 ../fastqs/SRR8505407_1_100.fastq.gz ../fastqs/SRR8505407_2_100.fastq.gz -->
19 <command detect_errors="aggressive"><![CDATA[ 19 <command detect_errors="aggressive"><![CDATA[
20 snakemake --snakefile "$__tool_directory__/Snakefile" 20 run_mr_snakemake.sh "$__tool_directory__/Snakefile"
21 -j \${GALAXY_SLOTS:-4} 21 \${GALAXY_SLOTS:-4}
22 --config 22 "$index_source.fields.path"
23 "$index_source.fields.path/$index_source.fields.name/gtf/exons.bed"
24 "."
25 "./tmp"
26 "$index_source.fields.name"
23 #if str($singlePaired.sPaired) == "paired_collection" 27 #if str($singlePaired.sPaired) == "paired_collection"
24 inputs="$singlePaired.input.forward,$singlePaired.input.reverse" 28 "$singlePaired.input.forward,$singlePaired.input.reverse"
25 #if $singlePaired.input.forward.is_of_type("fastq.gz"): 29 #if $singlePaired.input.forward.is_of_type("fastq.gz"):
26 compressed=1 30 "compressed=1"
27 #end if 31 #end if
28 #else 32 #else
29 inputs="$singlePaired.input1" 33 "$singlePaired.input1"
30 #if str($singlePaired.sPaired) == "paired" 34 #if str($singlePaired.sPaired) == "paired"
31 inputs="$singlePaired.input1,$singlePaired.input2" 35 inputs="$singlePaired.input1,$singlePaired.input2"
32 #end if 36 #end if
33 #if $singlePaired.input1.is_of_type("fastq.gz"): 37 #if $singlePaired.input1.is_of_type("fastq.gz"):
34 compressed=1 38 "compressed=1"
35 #end if 39 #end if
36 #end if 40 #end if
37 ref="$index_source.fields.path"
38 exon_bed="$index_source.fields.path/$index_source.fields.name/gtf/exons.bed"
39 genome="$index_source.fields.name"
40 output="."
41 temp="./tmp"
42 ]]></command> 41 ]]></command>
43 <inputs> 42 <inputs>
44 <!-- FASTQ input(s) and options specifically for paired-end data. --> 43 <!-- FASTQ input(s) and options specifically for paired-end data. -->
45 <conditional name="singlePaired"> 44 <conditional name="singlePaired">
46 <param name="sPaired" type="select" label="Single-end or paired-end reads"> 45 <param name="sPaired" type="select" label="Single-end or paired-end reads">