Mercurial > repos > iuc > migmap
diff migmap.xml @ 5:2c9f2a24f7a4 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap commit 35f97047b98a6444509bee371394188c1967265c"
| author | iuc |
|---|---|
| date | Mon, 29 Mar 2021 22:16:41 +0000 |
| parents | 29ec7b3a458b |
| children |
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--- a/migmap.xml Fri Nov 20 14:26:40 2020 +0000 +++ b/migmap.xml Mon Mar 29 22:16:41 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy1"> +<tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy2" profile="20.01"> <description>mapper for full-length T- and B-cell repertoire sequencing </description> <macros> @@ -16,9 +16,14 @@ #if $input.is_of_type('fasta') : ln -s '$input' in.fa && -#else +#else if $input.is_of_type('fasta.gz') : + ln -s '$input' in.fa.gz && +#else if $input.is_of_type('fastq') : ln -s '$input' in.fq && +#else if $input.is_of_type('fastq.gz') : + ln -s '$input' in.fq.gz #end if + migmap $allow_incomplete $allow_no_cdr3 @@ -91,6 +96,16 @@ <output name="output" file="test_stop_codon.out"/> </test> <test> + <param name="input" value="test_stop_codon.fq.gz" ftype="fastqsanger.gz"/> + <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" lines_diff="2"/> + </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"/>