Mercurial > repos > iuc > last
diff maf-convert.xml @ 0:9a7e91fc6562 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
author | iuc |
---|---|
date | Wed, 17 Jun 2020 14:50:21 -0400 |
parents | |
children | 8705e0d74a0f |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maf-convert.xml Wed Jun 17 14:50:21 2020 -0400 @@ -0,0 +1,143 @@ +<tool id="last_maf_convert" name="MAF-convert" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01"> + + <description>read MAF-format alignments and write them in another format.</description> + + <macros> + <import>macros_last.xml</import> + </macros> + + <requirements> + <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ + maf-convert + + $maf_convert.output_type.output_format + + $maf_convert.noheader + + #if $maf_convert.output_type.output_format == 'psl' + $maf_convert.output_type.protein + -j $maf_convert.output_type.j + #end if + + #if $maf_convert.output_type.output_format == 'sam' + $maf_convert.output_type.sam_file.dictionary + #if $maf_convert.output_type.sam_file.dictionary == '-d' + -f $maf_convert.output_type.sam_file.f + #end if + #if $maf_convert.output_type.readfile != '' + -r $maf_convert.output_type.r + #end if + #end if + + #if $maf_convert.output_type.output_format == 'blast' or $maf_convert.output_type.output_format == 'html' + -l $maf_convert.output_type.l + #end if + + '$maf_file' + + > '$outfile' + + ]]></command> + <inputs> + <param name="maf_file" type="data" format="maf" label="MAF file to convert" /> + + <section name="maf_convert" title="MAF-convert arguments" expanded="true"> + + <param name="noheader" argument="-n" type="boolean" truevalue="-n" falsevalue="" checked="false" label="No header." help="Omit any header lines from the output"/> + + <conditional name="output_type"> + <param name="output_format" type="select" multiple="false" label="Output format"> + <option value="axt">axt</option> + <option value="blast">blast</option> + <option value="blasttab">blasttab</option> + <option value="chain">chain</option> + <option value="html">html</option> + <option value="psl" selected="true">psl</option> + <option value="sam">sam</option> + <option value="tab">tab</option> + </param> + <when value="blast"> + <param argument="-l" type="integer" value="60" label="Line length"/> + </when> + <when value="html"> + <param argument="-l" type="integer" value="60" label="Line length"/> + </when> + <when value="psl"> + <param name="protein" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Protein alignments." /> + <param argument="-j" type="integer" value="1" label="Join neighboring alignments" help="Join neighboring alignments if they are co-linear and separated by at most N letters."/> + </when> + <when value="sam"> + <conditional name="sam_file"> + <param name="dictionary" argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false" label="Include dictionary of sequence lengths in sam format"/> + <when value="-d"> + <param argument="-f" type="data" format="dict" label="Get a sequence dictionary from DICTFILE" /> + </when> + </conditional> + <param argument="-r" type="text" value="" label="Specify read group information" help="Example: 'ID:1 PL:ILLUMINA SM:mysample'"/> + </when> + </conditional> + </section> + </inputs> + + <outputs> + <data format="maf" name="outfile" label="${on_string} to ${maf_convert.output_type.output_format}"> + <change_format> + <when input="maf_convert.output_type.output_format" value="axt" format="axt" /> + <when input="maf_convert.output_type.output_format" value="blast" format="blastxml" /> + <when input="maf_convert.output_type.output_format" value="blasttab" format="blastxml" /> + <when input="maf_convert.output_type.output_format" value="chain" format="txt" /> + <when input="maf_convert.output_type.output_format" value="html" format="html" /> + <when input="maf_convert.output_type.output_format" value="psl" format="tabular" /> + <when input="maf_convert.output_type.output_format" value="sam" format="sam" /> + <when input="maf_convert.output_type.output_format" value="tab" format="tabular" /> + </change_format> + </data> + </outputs> + + <tests> + <test> + <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/> + <section name="maf_convert"> + <conditional name="output_type"> + <param name="output_format" value="axt"/> + </conditional> + </section> + <output name="outfile" file="outfile_convert.axt"/> + </test> + <test> + <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/> + <section name="maf_convert"> + <conditional name="output_type"> + <param name="output_format" value="blast"/> + </conditional> + </section> + <output name="outfile" file="outfile_convert.blast"/> + </test> + <test> + <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/> + <section name="maf_convert"> + <conditional name="output_type"> + <param name="output_format" value="html"/> + </conditional> + </section> + <output name="outfile" file="outfile_convert.html"/> + </test> + <test> + <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/> + <section name="maf_convert"> + <conditional name="output_type"> + <param name="output_format" value="tab"/> + </conditional> + </section> + <output name="outfile" file="outfile_convert.tab"/> + </test> + </tests> + + <help><![CDATA[ + This script reads alignments in maf format, and writes them in another format. It can write them in these formats: axt, blast, blasttab, chain, html, psl, sam, tab. + ]]></help> + <citations><expand macro="citations"/></citations> +</tool>