Mercurial > repos > iuc > tetoolkit_tetranscripts
diff tetranscript.xml @ 2:bbeab8445490 draft
"planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 52fd61119be10e02b66852d5ccf21f4f1904b8c3"
| author | iuc |
|---|---|
| date | Sun, 04 Oct 2020 09:53:49 +0000 |
| parents | bf4ee2810759 |
| children | 313414e9abcf |
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--- a/tetranscript.xml Thu Jul 16 08:04:29 2020 -0400 +++ b/tetranscript.xml Sun Oct 04 09:53:49 2020 +0000 @@ -1,57 +1,58 @@ <?xml version="1.0"?> -<tool id="tetoolkit_tetranscripts" name="TEtranscripts" version="@TOOL_VERSION@+galaxy0"> +<tool id="tetoolkit_tetranscripts" name="TEtranscripts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>annotates reads to genes and transposable elements</description> <macros> - <token name="@TOOL_VERSION@">2.2.0</token> + <token name="@TOOL_VERSION@">2.2.1</token> + <token name="@VERSION_SUFFIX@">0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">tetranscripts</requirement> </requirements> <version_command>TEtranscripts --version</version_command> <command detect_errors="exit_code"><![CDATA[ - ## initialize - ## file extension is required - ln -s '$GTF' 'gene_annotation.gtf' && - ln -s '$TE' 'transposable_annotation.gtf' && +## initialize +## file extension is required +ln -s '$GTF' 'gene_annotation.gtf' && +ln -s '$TE' 'transposable_annotation.gtf' && - ## run - TEtranscripts - ## required - -t - #for $s in $sample_rep - '${s.t}' - #end for - -c - #for $s in $sample_rep - '${s.c}' - #end for - --GTF 'gene_annotation.gtf' - --TE 'transposable_annotation.gtf' - ## optional - --stranded '$io.stranded' - $io.sortByPos - --project 'result' - --mode '$ap.mode' - --minread $ap.minread - #if $ap.fragmentLength - --fragmentLength $ap.fragmentLength - #end if - --iteration $ap.iteration - --padj $ap.padj - --foldchange $ap.foldchange - #if 'log' in $ap.out - --verbose 3 - |& tee log.txt - #end if +## run +TEtranscripts +## required +-t +#for $s in $sample_rep + '${s.t}' +#end for +-c +#for $s in $sample_rep + '${s.c}' +#end for +--GTF 'gene_annotation.gtf' +--TE 'transposable_annotation.gtf' +## optional +--stranded '$io.stranded' +$io.sortByPos +--project 'result' +--mode '$ap.mode' +--minread $ap.minread +#if $ap.fragmentLength + --fragmentLength $ap.fragmentLength +#end if +--iteration $ap.iteration +--padj $ap.padj +--foldchange $ap.foldchange +#if 'log' in $oo.out + --verbose 3 + |& tee '$out_log' +#end if ]]></command> <inputs> <repeat name="sample_rep" min="2" title="Select input data"> <param argument="-t" type="data" format="bam" label="Treatment sample file"/> <param argument="-c" type="data" format="bam" label="Control sample file"/> </repeat> - <param argument="--GTF" type="data" format="gtf" label="Select GTF file for gene annotations"/> - <param argument="--TE" type="data" format="gtf" label="Select GTF file for transposable element annotations"/> - <section name="io" title="Input options"> + <param argument="--GTF" type="data" format="gtf" label="Select file for gene annotations"/> + <param argument="--TE" type="data" format ="gtf" label="Select file for transposable element annotations"/> + <section name="io" title="Input options" expanded="true"> <param argument="--stranded" type="select" label="Select library type"> <option value="no">Library is unstranded (no)</option> <option value="forward">Second-strand cDNA library e.g. QIAseq stranded (forward)</option> @@ -69,30 +70,32 @@ <param argument="--iteration" type="integer" value="100" min="0" label="Set maximum number of iterations used to optimize multi-reads assignment"/> <param argument="--padj" type="float" value="0.05" min="0.0" max="1.0" label="Set FDR cutoff for significance"/> <param argument="--foldchange" type="float" value="1.0" min="0.0" label="Set fold-change ratio (absolute) cutoff for differential expression"/> - <param name="out" type="select" multiple="true" label="Select output file(s)" help="Result files for gene TE analysis and sigDiff gene TE will be created if more than one dataset is applied."> + </section> + <section name="oo" title="Output options"> + <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="Result files for gene TE analysis and sigDiff gene TE will be created if more than one dataset is applied."> <option value="cnttable" selected="true">cntTable</option> - <option value="deseq2" selected="true">DESeq2.R</option> + <option value="deseq2">DESeq2.R</option> <option value="gta" selected="true">Gene TE Analysis</option> + <option value="log">Log</option> <option value="sgt" selected="true">SigDiff Gene TE</option> - <option value="log">Log</option> </param> </section> </inputs> <outputs> <data name="out_cnt" format="tabular" from_work_dir="result.cntTable" label="${tool.name} on ${on_string}: cntTable"> - <filter>'cnttable' in ap['out']</filter> + <filter>'cnttable' in oo['out']</filter> </data> <data name="out_deseq2" format="txt" from_work_dir="result_DESeq2.R" label="${tool.name} on ${on_string}: DESeq2.R"> - <filter>'deseq2' in ap['out']</filter> + <filter>'deseq2' in oo['out']</filter> + </data> + <data name="out_gta" format="tabular" from_work_dir="result_gene_TE_analysis.txt" label="${tool.name} on ${on_string}: Gene TE analysis"> + <filter>'gta' in oo['out']</filter> </data> <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log"> - <filter>'log' in ap['out']</filter> + <filter>'log' in oo['out']</filter> </data> - <data name="out_gta" format="txt" from_work_dir="result_gene_TE_analysis.txt" label="${tool.name} on ${on_string}: Gene TE analysis"> - <filter>'gta' in ap['out']</filter> - </data> - <data name="out_sgt" format="txt" from_work_dir="result_sigdiff_gene_TE.txt" label="${tool.name} on ${on_string}: SigDiff Gene TE"> - <filter>'sgt' in ap['out']</filter> + <data name="out_sgt" format="tabular" from_work_dir="result_sigdiff_gene_TE.txt" label="${tool.name} on ${on_string}: SigDiff Gene TE"> + <filter>'sgt' in oo['out']</filter> </data> </outputs> <tests> @@ -103,7 +106,7 @@ --> <!-- #1: default --> - <test expect_num_outputs="5"> + <test expect_num_outputs="3"> <repeat name="sample_rep"> <param name="t" value="treatment1.bam"/> <param name="c" value="control1.bam"/> @@ -114,39 +117,20 @@ </repeat> <param name="GTF" value="gtf.gtf"/> <param name="TE" value="te.gtf"/> - <section name="ap"> - <param name="out" value="cnttable,deseq2,gta,sgt,log"/> - </section> <output name="out_cnt"> <assert_contents> <has_n_lines n="295"/> - <!-- depends on sample names --> <has_text_matching expression="gene.+"/> - <!-- order changes --> <has_text_matching expression="TIRANT.+"/> </assert_contents> </output> - <output name="out_deseq2"> - <assert_contents> - <has_n_lines n="14"/> - <has_text_matching expression="data.+"/> - </assert_contents> - </output> - <output name="out_log"> - <assert_contents> - <has_text_matching expression="INFO"/> - <has_text_matching expression=".+Done"/> - </assert_contents> - </output> <output name="out_gta"> <assert_contents> <has_n_lines n="71"/> <has_line line="baseMean	log2FoldChange	lfcSE	stat	pvalue	padj"/> - <!-- order changes --> <has_text_matching expression="TIRANT.+"/> </assert_contents> </output> - <!-- no content, test dataset to small --> <output name="out_sgt"> <assert_contents> <has_n_lines n="1"/> @@ -177,14 +161,14 @@ <param name="iteration" value="90"/> <param name="padj" value="0.06"/> <param name="foldchange" value="2.0"/> + </section> + <section name="oo"> <param name="out" value="cnttable,deseq2,gta,sgt,log"/> </section> <output name="out_cnt"> <assert_contents> <has_n_lines n="295"/> - <!-- depends on sample names --> <has_text_matching expression="gene.+"/> - <!-- order changes --> <has_text_matching expression="TIRANT.+"/> </assert_contents> </output> @@ -194,20 +178,18 @@ <has_text_matching expression="data.+"/> </assert_contents> </output> + <output name="out_gta"> + <assert_contents> + <has_n_lines n="3"/> + <has_line line="baseMean	log2FoldChange	lfcSE	stat	pvalue	padj"/> + <has_text_matching expression="DNAREP1.+"/> + </assert_contents> + </output> <output name="out_log"> <assert_contents> <has_text_matching expression="INFO.+"/> </assert_contents> </output> - <output name="out_gta"> - <assert_contents> - <has_n_lines n="3"/> - <has_line line="baseMean	log2FoldChange	lfcSE	stat	pvalue	padj"/> - <!-- order changes --> - <has_text_matching expression="DNAREP1.+"/> - </assert_contents> - </output> - <!-- no content, test dataset to small --> <output name="out_sgt"> <assert_contents> <has_n_lines n="1"/> @@ -230,15 +212,13 @@ <section name="io"> <param name="stranded" value="reverse"/> </section> - <section name="ap"> + <section name="oo"> <param name="out" value="cnttable,deseq2,gta,sgt,log"/> </section> <output name="out_cnt"> <assert_contents> <has_n_lines n="295"/> - <!-- depends on sample names --> <has_text_matching expression="gene.+"/> - <!-- order changes --> <has_text_matching expression="TIRANT.+"/> </assert_contents> </output> @@ -248,19 +228,18 @@ <has_text_matching expression="data.+"/> </assert_contents> </output> - <output name="out_log"> - <assert_contents> - <has_text_matching expression="INFO.+"/> - </assert_contents> - </output> <output name="out_gta"> <assert_contents> <has_n_lines n="23"/> <has_line line="baseMean	log2FoldChange	lfcSE	stat	pvalue	padj"/> - <!-- order changes --> <has_text_matching expression="TART.+"/> </assert_contents> </output> + <output name="out_log"> + <assert_contents> + <has_text_matching expression="INFO.+"/> + </assert_contents> + </output> <output name="out_sgt"> <assert_contents> <has_n_lines n="2"/> @@ -289,7 +268,7 @@ **References** -More information are available on the `project website <http://hammelllab.labsites.cshl.edu/software/#TEtranscripts>`_ and `github <https://github.com/mhammell-laboratory/TEtranscripts>`_. +More information are available on the `project website <http://hammelllab.labsites.cshl.edu/software/#TEtranscripts>`_ and `GitHub <https://github.com/mhammell-laboratory/TEtranscripts>`_. ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btv422</citation>