Mercurial > repos > iuc > stringtie
diff stringtie_merge.xml @ 11:6e45b443ef1f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf
author | iuc |
---|---|
date | Thu, 01 Jun 2017 12:16:04 -0400 |
parents | c84d44519b2e |
children | dd4df992d93d |
line wrap: on
line diff
--- a/stringtie_merge.xml Tue Apr 04 12:58:27 2017 -0400 +++ b/stringtie_merge.xml Thu Jun 01 12:16:04 2017 -0400 @@ -1,17 +1,16 @@ -<tool id="stringtie_merge" name="StringTie" version="1.3.3"> - <description>merge transcripts</description> +<tool id="stringtie_merge" name="StringTie merge" version="1.3.3"> + <description>transcripts</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> - <command> - <![CDATA[ + <command><![CDATA[ stringtie --merge -p \${GALAXY_SLOTS:-1} #if $guide_gff: - -G "$guide_gff" + -G '$guide_gff' #end if -m $min_len -c $min_cov @@ -20,38 +19,37 @@ -f $min_iso -g $gap_len $keep_introns - #set inputs = '" "'.join(str($input_gtf).split(',')) - -o $out_gtf "$inputs" - ]]> - </command> + #set inputs = "' '".join(str($input_gtf).split(',')) + -o '$out_gtf' '$inputs' + ]]></command> <inputs> - <param type="data" name="input_gtf" multiple="True" format="gtf,gff3" /> - <param type="data" name="guide_gff" optional="True" format="gtf,gff3" /> - <param argument="-m" type="integer" name="min_len" value="50" help="Minimum input transcript length to include in the merge" /> - <param argument="-c" type="integer" name="min_cov" value="0" help="Minimum input transcript coverage to include in the merge" /> - <param argument="-F" type="float" name="min_fpkm" value="1.0" help="Minimum input transcript FPKM to include in the merge" /> - <param argument="-T" type="float" name="min_tpm" value="1.0" help="Minimum input transcript TPM to include in the merge" /> - <param argument="-f" type="float" name="min_iso" value="0.01" help="Minimum isoform fraction" /> - <param argument="-g" type="integer" name="gap_len" value="250" help="Gap between transcripts to merge together" /> - <param argument="-i" type="boolean" truevalue="-i" falsevalue="" name="keep_introns" help="Keep merged transcripts with retained introns" /> + <param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format" /> + <param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging" /> + <param name="min_len" argument="-m" type="integer" value="50" label="Minimum input transcript length to include in the merge" /> + <param name="min_cov" argument="-c" type="integer" value="0" label="Minimum input transcript coverage to include in the merge" /> + <param name="min_fpkm" argument="-F" type="float" value="1.0" label="Minimum input transcript FPKM to include in the merge" /> + <param name="min_tpm" argument="-T" type="float" value="1.0" label="Minimum input transcript TPM to include in the merge" /> + <param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction" /> + <param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together" /> + <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them" /> </inputs> <outputs> <data name="out_gtf" format="gtf" /> </outputs> <tests> <test> - <param ftype="gtf" name="input_gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" /> - <param ftype="gtf" name="guide_gff" value="stringtie_in.gtf" /> - <output file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2" name="out_gtf" /> + <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" /> + <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf" /> + <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2" /> </test> <test> - <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> - <param ftype="gtf" name="guide_gff" value="stringtie_merge_in3.gtf" /> - <output file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="2" name="out_gtf" /> + <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> + <param name="guide_gff" ftype="gtf" value="stringtie_merge_in3.gtf" /> + <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="2" /> </test> <test> - <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> - <output ftype="gtf" name="out_gtf"> + <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> + <output name="out_gtf" ftype="gtf"> <assert_contents> <has_text text="stringtie --merge" /> </assert_contents> @@ -59,35 +57,13 @@ </test> </tests> <help><![CDATA[ - **What it does?** -This is a special usage mode of StringTie_, distinct from the assembly usage mode. In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples. +This is a special usage mode of StringTie_, distinct from the assembly usage mode. In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples. -If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts. +If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts. .. _StringTie: http://ccb.jhu.edu/software/stringtie/ - ------- - -StringTie --merge has the following options:: - - -G <guide_gff> reference annotation to include in the merging (GTF/GFF3) - -o <out_gtf> output file name for the merged transcripts GTF - (default: stdout) - -m <min_len> minimum input transcript length to include in the merge - (default: 50) - -c <min_cov> minimum input transcript coverage to include in the merge - (default: 0) - -F <min_fpkm> minimum input transcript FPKM to include in the merge - (default: 1.0) - -T <min_tpm> minimum input transcript TPM to include in the merge - (default: 1.0) - -f <min_iso> minimum isoform fraction (default: 0.01) - -g <gap_len> gap between transcripts to merge together (default: 250) - -i keep merged transcripts with retained introns; by default - these are not kept unless there is strong evidence for them - -l <label> name prefix for output transcripts (default: MSTRG) ]]></help> <expand macro="citations" /> </tool>