Mercurial > repos > iuc > samtools_fastx
diff samtools_fastx.xml @ 2:720217c23995 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
| author | iuc |
|---|---|
| date | Tue, 28 Sep 2021 16:13:01 +0000 |
| parents | a8d69aee190e |
| children | b3d99709fe1a |
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--- a/samtools_fastx.xml Fri Sep 28 04:39:19 2018 -0400 +++ b/samtools_fastx.xml Tue Sep 28 16:13:01 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy1"> +<tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>extract FASTA or FASTQ from alignment files</description> <macros> <import>macros.xml</import> @@ -7,10 +7,10 @@ <expand macro="stdio"/> <expand macro="version_command" /> <command><![CDATA[ -@ADDTHREADS@ +@ADDTHREADS@ ## name sort input file if neccessary #if not $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'): - samtools sort -@ \$addthreads -n '$input' > input && + samtools sort -@ \$addthreads -n '$input' -T "\${TMPDIR:-.}" > input && #else: ln -s '$input' input && #end if @@ -39,21 +39,15 @@ #if 'r2' in str($outputs): -2 reverse.$output_fmt_cond.output_fmt_select #end if -#if str($inclusive_filter) != 'None': - #set $filter = $inclusive_filter - @FLAGS@ - -f $flags -#end if -#if str($exclusive_filter) != 'None': - #set $filter = $exclusive_filter - @FLAGS@ - -F $flags -#end if -#if str($exclusive_filter) != 'None': - #set $filter = $exclusive_filter_all - @FLAGS@ - -G $flags -#end if +#set $filter = $inclusive_filter +@FLAGS@ +-f $flags +#set $filter = $exclusive_filter +@FLAGS@ +-F $flags +#set $filter = $exclusive_filter_all +@FLAGS@ +-G $flags #if 's' in str($outputs): -s singletons.$output_fmt_cond.output_fmt_select #end if @@ -75,12 +69,12 @@ #end if #end if -input +input #if str($outputs)=='None' or 'other' in str($outputs): ## since currently stdout in not zipped (samtools doesn't know about the extension) #if str($output_fmt_cond.output_fmt_select).endswith('.gz'): - | gzip - + | gzip - #end if > output.$output_fmt_cond.output_fmt_select && ln -s output.$output_fmt_cond.output_fmt_select output @@ -148,10 +142,10 @@ <option value="-N">always append /1 and /2 to read name</option> </param> <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set"> - <expand macro="flag_options" /> + <expand macro="flag_options"/> </param> <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set"> - <expand macro="flag_options" /> + <expand macro="flag_options" s256="true" s2048="true"/> </param> <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set"> <expand macro="flag_options" /> @@ -270,8 +264,8 @@ <output name="forward" file="samtools_fastx-out3-2.fasta" ftype="fasta" /> <output name="reverse" file="samtools_fastx-out3-3.fasta" ftype="fasta" /> </test> - <!-- 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 + <!-- 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> <param name="input" value="samtools_fastx-in1.bam" ftype="bam" /> @@ -279,7 +273,7 @@ <param name="output_fmt_select" value="fasta.gz" /> </conditional> <param name="outputs" value="other" /> - <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" compare="sim_size" /> + <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" decompress="true"/> </test> <test> <param name="input" value="samtools_fastx-in2.bam" ftype="bam" /> @@ -287,9 +281,9 @@ <param name="output_fmt_select" value="fastqsanger.gz" /> </conditional> <param name="outputs" value="r0,r1,r2" /> - <output name="nonspecific" file="samtools_fastx-out2-1.fastq.gz" ftype="fastqsanger.gz" /> - <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" /> - <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" /> + <output name="nonspecific" file="samtools_fastx-out2-1.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> + <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> <param name="input" value="samtools_fastx-in3.sam" ftype="sam" /> @@ -297,9 +291,9 @@ <param name="output_fmt_select" value="fasta.gz" /> </conditional> <param name="outputs" value="r0,r1,r2" /> - <output name="nonspecific" file="samtools_fastx-out3-1.fasta.gz" ftype="fasta.gz" /> - <output name="forward" file="samtools_fastx-out3-2.fasta.gz" ftype="fasta.gz" /> - <output name="reverse" file="samtools_fastx-out3-3.fasta.gz" ftype="fasta.gz" /> + <output name="nonspecific" file="samtools_fastx-out3-1.fasta.gz" ftype="fasta.gz" decompress="true" /> + <output name="forward" file="samtools_fastx-out3-2.fasta.gz" ftype="fasta.gz" decompress="true" /> + <output name="reverse" file="samtools_fastx-out3-3.fasta.gz" ftype="fasta.gz" decompress="true" /> </test> <!-- tests from: https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2313--> <!--# basic 2 output test without singleton tracking--> @@ -476,12 +470,16 @@ <param name="ilumina_casava" value="-i" /> </conditional> <param name="outputs" value="r1,r2,s,other" /> + <conditional name="idxout_cond"> + <param name="idxout_select" value="yes"/> + <param name="index_format" value="n2i2"/> + </conditional> <param name="copy_tags" value="-t" /> <param name="copy_arb_tags" value="MD,ia" /> <param name="read_numbering" value="-N"/> - <output name="forward" file="7.1.fq.expected" ftype="fastqsanger" /> - <output name="reverse" file="7.2.fq.expected" ftype="fastqsanger" /> - <output name="singletons" file="7.s.fq.expected" ftype="fastqsanger" /> + <output name="forward" file="11.1.fq.expected" ftype="fastqsanger" /> + <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" /> </test> <!--# -i flag with index-->