Mercurial > repos > iuc > samtools_fastx
diff samtools_fastx.xml @ 4:66e23b11feae draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit cd62639660bef041ba14ecff337fb98e84e75d8a
| author | iuc |
|---|---|
| date | Mon, 20 Nov 2023 22:15:18 +0000 |
| parents | b3d99709fe1a |
| children |
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--- a/samtools_fastx.xml Mon Aug 15 09:16:56 2022 +0000 +++ b/samtools_fastx.xml Mon Nov 20 22:15:18 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>extract FASTA or FASTQ from alignment files</description> <macros> <import>macros.xml</import> @@ -160,7 +160,7 @@ <when value="yes"> <param name="write1st" argument="--i1" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="write first index reads to extra data set" /> <param name="write2nd" argument="--i2" type="boolean" truevalue="yes" falsevalue="no" checked='true' label="write second index reads to extra data set" /> - <param name="index_format" argument="--index-format" type="text" label="Index format: How to parse barcode and quality tags"> + <param argument="--index-format" type="text" label="Index format: How to parse barcode and quality tags"> <help> The index-format string describes how to parse the barcode and quality tags, for example: i14i8 the first 14 characters are index 1, the next 8 characters are index 2 @@ -171,8 +171,8 @@ of the tag as index 1 </help> </param> - <param name="barcode_tag" argument="--barcode-tag" type="text" optional="True" label="Barcode tag [default: BC]"/> - <param name="quality_tag" argument="--quality-tag" type="text" optional="True" label="Quality tag [default: QT]"/> + <param argument="--barcode-tag" type="text" optional="True" label="Barcode tag [default: BC]"/> + <param argument="--quality-tag" type="text" optional="True" label="Quality tag [default: QT]"/> </when> </conditional> </inputs> @@ -236,7 +236,7 @@ </outputs> <tests> <!-- tests from original Galaxy tool --> - <test> + <test expect_num_outputs="1"> <param name="input" value="samtools_fastx-in1.bam" ftype="bam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fasta" /> @@ -244,7 +244,7 @@ <param name="outputs" value="other" /> <output name="output" file="samtools_fastx-out1.fasta" ftype="fasta" /> </test> - <test> + <test expect_num_outputs="3"> <param name="input" value="samtools_fastx-in2.bam" ftype="bam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger" /> @@ -254,7 +254,7 @@ <output name="forward" file="samtools_fastx-out2-2.fastq" ftype="fastqsanger" /> <output name="reverse" file="samtools_fastx-out2-3.fastq" ftype="fastqsanger" /> </test> - <test> + <test expect_num_outputs="3"> <param name="input" value="samtools_fastx-in3.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fasta" /> @@ -267,7 +267,7 @@ <!-- tests from original Galaxy tool with gz output. for some reason gzip (which is used for compressing stdout does not give exactly the same file contents .. the other compressed files seem to)--> - <test> + <test expect_num_outputs="1"> <param name="input" value="samtools_fastx-in1.bam" ftype="bam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fasta.gz" /> @@ -275,7 +275,7 @@ <param name="outputs" value="other" /> <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" decompress="true"/> </test> - <test> + <test expect_num_outputs="3"> <param name="input" value="samtools_fastx-in2.bam" ftype="bam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger.gz" /> @@ -285,7 +285,7 @@ <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> </test> - <test> + <test expect_num_outputs="3"> <param name="input" value="samtools_fastx-in3.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fasta.gz" /> @@ -298,7 +298,7 @@ <!-- tests from: https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2313--> <!--# basic 2 output test without singleton tracking--> <!--test_cmd($opts, out=>'bam2fq/1.stdout.expected', out_map=>{'1.fq' => 'bam2fq/1.1.fq.expected', '2.fq' => 'bam2fq/1.2.fq.expected'},cmd=>"$$opts{bin}/samtools fastq @$threads -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");--> - <test> + <test expect_num_outputs="3"> <param name="input" value="bam2fq.001.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger" /> @@ -310,7 +310,7 @@ </test> <!--# basic 2 output test with singleton tracking but no singleton--> <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/2.1.fq.expected', '2.fq' => 'bam2fq/2.2.fq.expected', 's.fq' => 'bam2fq/2.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");--> - <test> + <test expect_num_outputs="4"> <param name="input" value="bam2fq.001.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger" /> @@ -323,7 +323,7 @@ </test> <!--# basic 2 output test with singleton tracking with a singleton in the middle--> <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/3.1.fq.expected', '2.fq' => 'bam2fq/3.2.fq.expected', 's.fq' => 'bam2fq/3.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.002.sam");--> - <test> + <test expect_num_outputs="4"> <param name="input" value="bam2fq.002.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger" /> @@ -336,7 +336,7 @@ </test> <!--# basic 2 output test with singleton tracking with a singleton as last read--> <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.003.sam");--> - <test> + <test expect_num_outputs="4"> <param name="input" value="bam2fq.003.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger" /> @@ -349,7 +349,7 @@ </test> <!--# tag output test with singleton tracking with a singleton as last read--> <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");--> - <test> + <test expect_num_outputs="5"> <param name="input" value="bam2fq.004.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger" /> @@ -357,7 +357,8 @@ <param name="outputs" value="r1,r2,s,other" /> <conditional name="idxout_cond"> <param name="idxout_select" value="yes"/> - <param name="write1st" value="yes"/> + <param name="write1st" value="true"/> + <param name="write2nd" value="false"/> <param name="barcode_tag" value="BC"/> <param name="index_format" value="n2i2"/> </conditional> @@ -369,7 +370,7 @@ </test> <!--# test -O flag with no OQ tags--> <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");--> - <test> + <test expect_num_outputs="5"> <param name="input" value="bam2fq.010.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger" /> @@ -378,7 +379,8 @@ <param name="outputs" value="r1,r2,s,other" /> <conditional name="idxout_cond"> <param name="idxout_select" value="yes"/> - <param name="write1st" value="yes"/> + <param name="write1st" value="true"/> + <param name="write2nd" value="false"/> <param name="barcode_tag" value="BC"/> <param name="index_format" value="n2i2"/> </conditional> @@ -390,7 +392,7 @@ </test> <!--# test -O flag with OQ tags--> <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/10.1.fq.expected', '2.fq' => 'bam2fq/10.2.fq.expected', 's.fq' => 'bam2fq/10.s.fq.expected', 'bc.fq' => 'bam2fq/bc10.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.010.sam");--> - <test> + <test expect_num_outputs="5"> <param name="input" value="bam2fq.010.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger" /> @@ -399,7 +401,8 @@ <param name="outputs" value="r1,r2,s,other" /> <conditional name="idxout_cond"> <param name="idxout_select" value="yes"/> - <param name="write1st" value="yes"/> + <param name="write1st" value="true"/> + <param name="write2nd" value="false"/> <param name="barcode_tag" value="BC"/> <param name="index_format" value="n2i2"/> </conditional> @@ -411,7 +414,7 @@ </test> <!--# tag output test with separators and -N flag--> <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/5.1.fq.expected', '2.fq' => 'bam2fq/5.2.fq.expected', 's.fq' => 'bam2fq/5.s.fq.expected', 'bc_split.fq' => 'bam2fq/bc_split.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -N \-\-index-format 'n*i*' \-\-i1 $$opts{path}/bc_split.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");--> - <test> + <test expect_num_outputs="5"> <param name="input" value="bam2fq.005.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger" /> @@ -420,7 +423,8 @@ <param name="read_numbering" value="-N"/> <conditional name="idxout_cond"> <param name="idxout_select" value="yes"/> - <param name="write1st" value="yes"/> + <param name="write1st" value="true"/> + <param name="write2nd" value="false"/> <param name="barcode_tag" value="BC"/> <param name="index_format" value="n*i*"/> </conditional> @@ -432,7 +436,7 @@ </test> <!--# -t flag--> <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/6.1.fq.expected', '2.fq' => 'bam2fq/6.2.fq.expected', 's.fq' => 'bam2fq/6.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");--> - <test> + <test expect_num_outputs="4"> <param name="input" value="bam2fq.005.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger" /> @@ -447,7 +451,7 @@ </test> <!--# -T flag--> <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");--> - <test> + <test expect_num_outputs="4"> <param name="input" value="bam2fq.005.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger" /> @@ -463,7 +467,7 @@ </test> <!--# -i flag with no index--> <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -i -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");--> - <test> + <test expect_num_outputs="6"> <param name="input" value="bam2fq.005.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger" /> @@ -481,10 +485,12 @@ <output name="reverse" file="11.2.fq.expected" ftype="fastqsanger" /> <output name="singletons" file="11.s.fq.expected" ftype="fastqsanger" /> <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> + <output name="i1" file="11.i.fq.expected" ftype="fastqsanger" /> + <output name="i2" file="11.i2.fq.expected" ftype="fastqsanger" /> </test> <!--# -i flag with index--> <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/8.1.fq.expected', '2.fq' => 'bam2fq/8.2.fq.expected', 's.fq' => 'bam2fq/8.s.fq.expected', 'i.fq' => 'bam2fq/8.i.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -i \-\-index-format 'n2i2' \-\-i1 $$opts{path}/i.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");--> - <test> + <test expect_num_outputs="6"> <param name="input" value="bam2fq.004.sam" ftype="sam" /> <conditional name="output_fmt_cond"> <param name="output_fmt_select" value="fastqsanger" /> @@ -493,7 +499,7 @@ <param name="outputs" value="r1,r2,s,other" /> <conditional name="idxout_cond"> <param name="idxout_select" value="yes"/> - <param name="write1st" value="yes"/> + <param name="write1st" value="true"/> <param name="barcode_tag" value="BC"/> <param name="index_format" value="n2i2"/> </conditional> @@ -502,6 +508,7 @@ <output name="singletons" file="8.s.fq.expected" ftype="fastqsanger" /> <output name="output" file="2.stdout.expected" ftype="fastqsanger" /> <output name="i1" file="8.i.fq.expected" ftype="fastqsanger" /> + <output name="i2" file="8.i2.fq.expected" ftype="fastqsanger" /> </test> </tests> <help><![CDATA[