# HG changeset patch
# User iuc
# Date 1506778386 14400
# Node ID cbf4a6ffc36908baf34fa1d280aa801b0e660000

planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa

diff -r 000000000000 -r cbf4a6ffc369 migmap.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/migmap.xml	Sat Sep 30 09:33:06 2017 -0400
@@ -0,0 +1,112 @@
+<tool id="migmap" name="MiGMAP" version="1.0.2.1">
+    <description>mapper for full-length T- and B-cell repertoire sequencing
+    </description>
+    <requirements>
+        <requirement type="package" version="1.0.2">migmap</requirement>
+    </requirements>
+    <command detect_errors='exit_code'><![CDATA[
+export IGBLAST_PATH=\$(dirname \$(which igblastn)) &&
+#if $input.is_of_type('fasta') :
+    ln -s '$input' in.fa &&
+#else
+    ln -s '$input' in.fq &&
+#end if
+migmap 
+    $allow_incomplete
+    $allow_no_cdr3
+    $allow_noncanonical
+    $allow_noncoding
+    $all_alleles
+    $by_read
+    #if str($qual_threshold):
+        -q $qual_threshold
+    #end if
+    -p "\${GALAXY_SLOTS:-4}"
+    --data-dir "\${IGBLAST_PATH}/../share/igblast"
+    -S $species 
+    -R $receptor_list
+    --report '$report'
+    #if $input.is_of_type('fasta'): 
+        in.fa
+    #else
+        in.fq
+    #end if
+    '$output'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" format="fasta,fastq"/>
+        <param type="select" name="species" label="Species" value='human'>
+            <option value='human' selected='true'>Human</option>
+            <option value='mouse'>Mouse</option>
+            <option value='rat'>Rat</option>
+            <option value='rabbit'>Rabbit</option>
+            <option value='rhesus_monkey'>Rhesus monkey</option>
+        </param>
+        <param type="select" name="receptor_list" label="Receptor and Chain" multiple='true' value='IGH'>
+            <option value='IGH' selected='true'>IGH</option>
+            <option value='IGL'>IGL</option>
+            <option value='IGK'>IGK</option>
+            <option value='TRA'>TRA</option>
+            <option value='TRB'>TRB</option>
+            <option value='TRG'>TRG</option>
+            <option value='TRD'>TRD</option>
+        </param>
+        <param name="qual_threshold" type="integer" label="Quality Theshold" optional="true"
+           help="Threshold for average quality of mutations and N-regions of CDR3 (only relevant for fastq input)"/>
+        <param name="allow_incomplete" type="boolean" label="Report clonotypes with partial CDR3 mapping" checked="false"
+           truevalue="--allow-incomplete" falsevalue=""/>
+        <param name="all_alleles" type="boolean"
+           label="use all alleles during alignemt (default = only major (*01) alleles)" checked='false'
+           truevalue="--all-alleles" falsevalue=""/>
+        <param name="allow_no_cdr3" type="boolean" label="Report clonotypes with no CDR3" checked='false'
+           truevalue="--allow-no-cdr3" falsevalue=""/>
+        <param name="allow_noncanonical" type="boolean" label="Report clonotypes that have non-canonical CDR3"
+           checked='false'
+           truevalue="--allow-noncanonical" falsevalue=""/>
+        <param name="allow_noncoding" type="boolean" label="Report non-coding clonotypes (stop codon or frameshift)"
+           checked='false'
+           truevalue="--allow-noncoding" falsevalue=""/>
+        <param name="by_read" type="boolean" label="Report mapping details for each read" checked='false'
+           truevalue="--by-read" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+        <data name="report" format="txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="test_stop_codon.fa"/>
+            <param name="allow_noncoding" value="--allow-noncoding"/>
+            <param name="by_read" value="--by-read"/>
+            <param name="allow_noncanonical" value="--allow-noncanonical"/>
+            <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
+            <param name="allow_incomplete" value="--allow-incomplete"/>
+            <param name="all_alleles" value="--all-alleles"/>
+            <output name="output" file="test_stop_codon.out"/>
+        </test>
+        <test>
+            <param name="allow_noncoding" value="--allow-noncoding"/>
+            <param name="by_read" value="--by-read"/>
+            <param name="input" value="test_out_of_frame.fa"/>
+            <output name="output" file="test_out_of_frame.out"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+    This software is a smart wrapper for the IgBlast V-(D)-J mapping tool designed to facilitate analysis immune
+    receptor libraries profiled using high-throughput sequencing
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+          @misc{githubmigmap,
+          author = {Shugay, Mikhail},
+          year = {2015},
+          title = {migmap},
+          publisher = {GitHub},
+          journal = {GitHub repository},
+          url = {https://github.com/mikessh/migmap},
+          }
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r cbf4a6ffc369 test-data/test_out_of_frame.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_out_of_frame.fa	Sat Sep 30 09:33:06 2017 -0400
@@ -0,0 +1,2 @@
+>CGTTCAGTTCTTTTGCG|PRCONS=Human-IGHD|SEQORIENT=F|CREGION=Human-IGHD-InternalC|CONSCOUNT=1|DUPCOUNT=1
+TTCAGACGTGTGCTCTTCCGATCTCTTGTTTATTATACAGGTCTACGGGGGACCTGGAGGATCCTCTTCTTGGTGGCAGCAGCAACAGGTGCCAACTCCCAGGTGCGGCTGGTGCAAGCTGGGTCGGAGTTGAAGAAGCCTGGGGCCTAAGTGTAGGGTTCCTGCAAGCCTTCTGGATACACCTTCACTAGCTCTGCTATGAATTGGGTGCGACCGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACACCAACACTGGGAACCCAACGTATGCCCAGGGCTTCACAGGACGGTTTGTCTTCTCCTTGGACACCTCTGTCAGCACGGCATATCTGCAGATCTGCAGCCTAAAGGCTGAGGACACTGCCGTGTATTACTGTGCGCCGGCTTGTGGTGGTGATTGCTATAGGACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCACCCACCAAGGCTCCGGATGTGTTCC
diff -r 000000000000 -r cbf4a6ffc369 test-data/test_out_of_frame.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_out_of_frame.out	Sat Sep 30 09:33:06 2017 -0400
@@ -0,0 +1,2 @@
+read.header	cdr3nt	cdr3aa	cdr.insert.qual	mutations.qual	v.segment	d.segment	j.segment	cdr1.start.in.read	cdr1.end.in.read	cdr2.start.in.read	cdr2.end.in.read	cdr3.start.in.read	cdr3.end.in.read	v.end.in.cdr3	d.start.in.cdr3	d.end.in.cdr3	j.start.in.cdr3	v.del	d.del.5	d.del.3	j.del	mutations.nt.FR1	mutations.nt.CDR1	mutations.nt.FR2	mutations.nt.CDR2	mutations.nt.FR3	mutations.nt.CDR3	mutations.nt.FR4	rc	complete	has.cdr3	in.frame	no.stop	mutations.aa.FR1	mutations.aa.CDR1	mutations.aa.FR2	mutations.aa.CDR2	mutations.aa.FR3	mutations.aa.CDR3	mutations.aa.FR4	pol.v	pol.d.5	pol.d.3	pol.j	canonical	contignt
+>CGTTCAGTTCTTTTGCG|PRCONS=Human-IGHD|SEQORIENT=F|CREGION=Human-IGHD-InternalC|CONSCOUNT=1|DUPCOUNT=1	TGTGCGCCGGCTTGTGGTGGTGATTGCTATAGGACAACTGGTTCGACCCCTGG	CAPACGGDtg?L*DNWFDPW	IIIIIIII	IIIIIIIIIII	IGHV7-4-1*01	IGHD2-21*01	IGHJ5*01	174	198	249	273	384	437	6	11	30	33	3	6	3	0	S7:A>G,S18:T>G,S26:T>G,S49:C>A,S54:A>T,S58:T>G,S69:G>C	S94:A>C	S115:A>C			S332:T>C	S343:A>G	false	true	true	false	false	S2:Q>R,S6:S>A,S8:S>S,S16:S>*,S18:K>*,S19:V>G,S23:A>P	S31:Y>S	S38:Q>P			S110:T>T	S114:K>R	-1	-1	-1	-1	true	CAGGTGCGGCTGGTGCAAGCTGGGTCGGAGTTGAAGAAGCCTGGGGCCTAAGTGTAGGGTTCCTGCAAGCCTTCTGGATACACCTTCACTAGCTCTGCTATGAATTGGGTGCGACCGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACACCAACACTGGGAACCCAACGTATGCCCAGGGCTTCACAGGACGGTTTGTCTTCTCCTTGGACACCTCTGTCAGCACGGCATATCTGCAGATCTGCAGCCTAAAGGCTGAGGACACTGCCGTGTATTACTGTGCGCCGGCTTGTGGTGGTGATTGCTATAGGACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCACCCACCAAGGCTCCGGATGTGTTCC
diff -r 000000000000 -r cbf4a6ffc369 test-data/test_stop_codon.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stop_codon.fa	Sat Sep 30 09:33:06 2017 -0400
@@ -0,0 +1,2 @@
+>AACATAGTAAATCAGTC|PRCONS=Human-IGHA|SEQORIENT=F|CREGION=Human-TRA-InternalC|CONSCOUNT=1|DUPCOUNT=1
+AACATCGTAAATCAGTCGATACGGGGGGCTCCGGGACTGCGGAGAACATATTGTGATGTTCGTGCCTCAGAGCTAAAACTATGAGTGAATTTCGGATTCACCATGACGTCAATGAACTGCTTAGCCTGCTGCGTGTCCACGGAGGAGATGGGGCTGAGGTCTACATTGACCTGCTTCAAAAGAACAGGACCCCGTACGTCACTACCACTGTCTCTGCTCACAGTGCCAAGAAGACTTTCTAAAGAAATATGATGAACTGAAATCTAAAAATACAAGGAACCTTGAACCGCAGCAGCACAC
diff -r 000000000000 -r cbf4a6ffc369 test-data/test_stop_codon.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_stop_codon.out	Sat Sep 30 09:33:06 2017 -0400
@@ -0,0 +1,2 @@
+read.header	cdr3nt	cdr3aa	cdr.insert.qual	mutations.qual	v.segment	d.segment	j.segment	cdr1.start.in.read	cdr1.end.in.read	cdr2.start.in.read	cdr2.end.in.read	cdr3.start.in.read	cdr3.end.in.read	v.end.in.cdr3	d.start.in.cdr3	d.end.in.cdr3	j.start.in.cdr3	v.del	d.del.5	d.del.3	j.del	mutations.nt.FR1	mutations.nt.CDR1	mutations.nt.FR2	mutations.nt.CDR2	mutations.nt.FR3	mutations.nt.CDR3	mutations.nt.FR4	rc	complete	has.cdr3	in.frame	no.stop	mutations.aa.FR1	mutations.aa.CDR1	mutations.aa.FR2	mutations.aa.CDR2	mutations.aa.FR3	mutations.aa.CDR3	mutations.aa.FR4	pol.v	pol.d.5	pol.d.3	pol.j	canonical	contignt
+>AACATAGTAAATCAGTC|PRCONS=Human-IGHA|SEQORIENT=F|CREGION=Human-TRA-InternalC|CONSCOUNT=1|DUPCOUNT=1	.	.			IGHV4-39*05	IGHD2/OR15-2a*01	IGHJ4*01	215	216	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	-1	S55:C>A,S57:C>G,S62:C>T,S63:T>A,S64:G>C							false	false	false	true	false	S18:S>Y,S19:L>V,S20:T>T,S21:C>T,S21:C>T							-1	-1	-1	-1	false	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGACCCCGTACGTCACTACCACTGTCTCTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN