| Next changeset 1:fbbe507e692b (2018-08-04) |
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Commit message:
planemo upload for repository https://github.com/mikessh/migmap commit 6d79114dd74ef2ee3071a100d1e8cd6d2df50caa |
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added:
migmap.xml test-data/test_out_of_frame.fa test-data/test_out_of_frame.out test-data/test_stop_codon.fa test-data/test_stop_codon.out |
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| diff -r 000000000000 -r b2f1cf977ca9 migmap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/migmap.xml Sat Sep 30 09:33:24 2017 -0400 |
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| @@ -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> |
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| diff -r 000000000000 -r b2f1cf977ca9 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 09:33:24 2017 -0400 |
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| @@ -0,0 +1,2 @@ +>CGTTCAGTTCTTTTGCG|PRCONS=Human-IGHD|SEQORIENT=F|CREGION=Human-IGHD-InternalC|CONSCOUNT=1|DUPCOUNT=1 +TTCAGACGTGTGCTCTTCCGATCTCTTGTTTATTATACAGGTCTACGGGGGACCTGGAGGATCCTCTTCTTGGTGGCAGCAGCAACAGGTGCCAACTCCCAGGTGCGGCTGGTGCAAGCTGGGTCGGAGTTGAAGAAGCCTGGGGCCTAAGTGTAGGGTTCCTGCAAGCCTTCTGGATACACCTTCACTAGCTCTGCTATGAATTGGGTGCGACCGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACACCAACACTGGGAACCCAACGTATGCCCAGGGCTTCACAGGACGGTTTGTCTTCTCCTTGGACACCTCTGTCAGCACGGCATATCTGCAGATCTGCAGCCTAAAGGCTGAGGACACTGCCGTGTATTACTGTGCGCCGGCTTGTGGTGGTGATTGCTATAGGACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGCACCCACCAAGGCTCCGGATGTGTTCC |
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| diff -r 000000000000 -r b2f1cf977ca9 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 09:33:24 2017 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r b2f1cf977ca9 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 09:33:24 2017 -0400 |
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| @@ -0,0 +1,2 @@ +>AACATAGTAAATCAGTC|PRCONS=Human-IGHA|SEQORIENT=F|CREGION=Human-TRA-InternalC|CONSCOUNT=1|DUPCOUNT=1 +AACATCGTAAATCAGTCGATACGGGGGGCTCCGGGACTGCGGAGAACATATTGTGATGTTCGTGCCTCAGAGCTAAAACTATGAGTGAATTTCGGATTCACCATGACGTCAATGAACTGCTTAGCCTGCTGCGTGTCCACGGAGGAGATGGGGCTGAGGTCTACATTGACCTGCTTCAAAAGAACAGGACCCCGTACGTCACTACCACTGTCTCTGCTCACAGTGCCAAGAAGACTTTCTAAAGAAATATGATGAACTGAAATCTAAAAATACAAGGAACCTTGAACCGCAGCAGCACAC |
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| diff -r 000000000000 -r b2f1cf977ca9 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 09:33:24 2017 -0400 |
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| @@ -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 |