diff filter_low_expr_transcripts.xml @ 0:6821f5ea01d8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_low_expr_transcripts.xml	Mon Aug 01 14:44:51 2016 -0400
@@ -0,0 +1,99 @@
+<tool id="trinity_filter_low_expr_transcripts" name="Filter low expression transcripts" version="@WRAPPER_VERSION@.0">
+    <description>from a Trinity assembly</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+        filter_low_expr_transcripts.pl
+            --matrix "$matrix"
+            --transcripts "$assembly"
+
+            #if $additional_params.gene_map.has_gene_map == "no":
+                --gene_trans_map $additional_params.gene_map.gene_trans_map
+            #else
+                --trinity_mode
+            #end if
+
+            #if str($min_expr_any):
+                --min_expr_any $min_expr_any
+            #end if
+
+            #if str($isoform_filter.highest_iso_only) == "yes":
+                --highest_iso_only
+            #else if str($isoform_filter.min_pct_dom_iso):
+                --min_pct_dom_iso $isoform_filter.min_pct_dom_iso
+            #end if
+
+            > "$filtered"
+    ]]></command>
+    <inputs>
+        <param format="fasta" name="assembly" argument="--transcripts" type="data" label="Trinity assembly"/>
+        <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix"/>
+
+        <param name="min_expr_any" type="float" argument="--min_expr_any" optional="true" label="Minimum expression level required across any sample"/>
+
+
+        <conditional name="isoform_filter">
+            <param name="highest_iso_only" argument="--highest_iso_only" type="select" label="Only retain the most highly expressed isoform per gene">
+                <option value="yes">Yes</option>
+                <option value="no" selected="true">No</option>
+            </param>
+            <when value="yes">
+            </when>
+            <when value="no">
+                <param name="min_pct_dom_iso" argument="--min_pct_dom_iso" type="integer" optional="true" label="Minimum percent of dominant isoform expression"/>
+            </when>
+        </conditional>
+
+        <section name="additional_params" title="Additional Options" expanded="False">
+            <conditional name="gene_map">
+                <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed">
+                    <option value="yes">Yes</option>
+                    <option value="no">No</option>
+                </param>
+                <when value="yes">
+                </when>
+                <when value="no">
+                    <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />
+                </when>
+            </conditional>
+
+        </section>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="filtered" label="${tool.name} on ${on_string}: filtered low expression transcripts"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix" value="filtered/counts.matrix"/>
+            <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
+            <param name="min_expr_any" value="25"/>
+            <output name="filtered" file="filtered/Trinity_filtered_exp.fasta" />
+        </test>
+        <!-- this option is broken in 2.2.0: https://github.com/trinityrnaseq/trinityrnaseq/issues/129
+        <test>
+            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
+            <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
+            <param name="isoform_filter|highest_iso_only" value="yes"/>
+            <output name="filtered" file="filtered/Trinity_filtered_hi_iso.fasta" />
+        </test-->
+        <test>
+            <param name="matrix" value="filtered/counts.matrix"/>
+            <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
+            <param name="isoform_filter|min_pct_dom_iso" value="20"/>
+            <output name="filtered" file="filtered/Trinity_filtered_pct_iso.fasta" />
+        </test>
+    </tests>
+    <help>
+        Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+        This tool filters a Trinity assembly using an expression matrix built
+        with "Build expression matrix for a de novo assembly of RNA-Seq data by Trinity" tool.
+        It discards transcripts/isoforms having a low expression level.
+
+        .. _Trinity: http://trinityrnaseq.github.io
+    </help>
+
+    <expand macro="citation" />
+</tool>