diff mitobim.xml @ 6:a03d23c6ab95 draft

MitoBim and interleave

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mitobim.xml	Thu Nov 02 12:44:55 2017 -0400
@@ -0,0 +1,77 @@
+<tool id="mitobim" name="MITObim" version="0.1.0">
+    <description>mitochondrial baiting and iterative mapping</description>
+    <requirements>
+        <requirement type="package" version="4.0.2">mira4_assembler</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+	cp $readpool readpool.fastq;
+        MITObim_1.8.pl
+        	--pair
+        	--quick $quick
+        	-start 1
+        	-end $end
+        	-sample $sample
+        	-ref $ref
+        	-readpool readpool.fastq
+        	--clean >& log;
+	rm readpool.fastq
+    ]]></command>
+    <inputs>
+        <param type="data" name="quick" format="fasta,txt" 
+        	   label="starts process with initial baiting using provided fasta reference" />
+        <param type="data" name="readpool" format="fastqsanger,fastq" 
+        	   label="readpool in fastq format (*.gz is also allowed) ! For pair-end reads, please use interleave tool to join the forward and revers reads into one fastq file. !" />
+        <param name="end" type="integer" label="iteration to end with, default=1" 
+               value="50" min="1" max="500" help="(-end)" />
+        <param name="sample" size="30" type="text" value="sample" label="sampleID as used in initial MIRA assembly"/>       
+        <param name="ref" size="30" type="text" value="reference" label="referenceID as used in initial MIRA assembly"/>       
+    </inputs>
+    <outputs>
+        <data name="output1" format="fasta" from_work_dir="finaloutput.fasta" label="${tool.name} on ${on_string}: Fasta"/>
+	<data name="output2" format="txt" from_work_dir="log" label="${tool.name} on ${on_string}: Log" />
+    </outputs>
+
+    <help><![CDATA[
+        
+MITObim - mitochondrial baiting and iterative mapping
+version 1.8
+author: Christoph Hahn, (c) 2012-2015
+
+usage: ./MITObim.pl <parameters>
+
+parameters:
+        -start <int>        iteration to start with, default=1
+        -end <int>      iteration to end with, default=1
+        -sample <string>    sampleID as used in initial MIRA assembly
+        -ref <string>       referenceID as used in initial MIRA assembly
+        -readpool <FILE>    readpool in fastq format (*.gz is also allowed)
+        -maf <FILE>     maf file from previous MIRA assembly
+
+optional:
+        --quick <FILE>      starts process with initial baiting using provided fasta reference
+        --kbait <int>       set kmer for baiting stringency (default: 31)
+        --denovo        runs MIRA in denovo mode (default: mapping)
+        --pair          finds pairs after baiting (relies on /1 and /2 header convention for read pairs) (default: no)
+        --verbose       show detailed output of MIRA modules (default: no)
+        --split         split reference at positions with more than 5N (default: no)
+        --help          shows this helpful information
+        --clean                 retain only the last 2 iteration directories (default: no)
+        --trimreads     trim data (default: no; we recommend to trim beforehand and feed MITObim with pre trimmed data)
+        --trimoverhang      trim overhang up- and downstream of reference (default: no)
+        --missmatch <int>   number of allowed missmatches in mapping - only for illumina data (default: 15% of avg. read length)
+        --min_cov <int>     minimum average coverage of contigs to be retained (default: off)
+        --mirapath <string>     full path to MIRA binaries (only needed if MIRA is not in PATH)
+        --iontor        use iontorrent data (experimental - default is illumina data)
+        --454           use 454 data (experimental - default is illumina data)
+
+examples:
+        ./MITObim.pl -start 1 -end 5 -sample StrainX -ref reference-mt -readpool illumina_readpool.fastq -maf initial_assembly.maf
+        ./MITObim.pl -end 10 --quick reference.fasta -sample StrainY -ref reference-mt -readpool illumina_readpool.fastq
+
+
+    ]]></help>
+
+</tool>