diff abundance_estimates_to_matrix.xml @ 10:13ab393ba794 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4

--- a/abundance_estimates_to_matrix.xml	Mon Jan 22 11:28:19 2018 -0500
+++ b/abundance_estimates_to_matrix.xml	Thu Jun 14 03:12:12 2018 -0400
@@ -1,12 +1,12 @@
-<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.2">
+<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@">
     <description>for a de novo assembly of RNA-Seq data by Trinity</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="3.20.1">bioconductor-edger</requirement>
+        <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
         <requirement type="package" version="0.9.1">salmon</requirement>
-        <requirement type="package" version="0.43.1">kallisto</requirement>
+        <requirement type="package" version="0.44.0">kallisto</requirement>
     </expand>
     <command detect_errors="aggressive"><![CDATA[
         #import re
@@ -19,13 +19,38 @@
         --est_method ${est_method}
         --cross_sample_norm ${additional_params.cross_sample_norm}
 
+        #if $gene_trans_map:
+            --gene_trans_map '$gene_trans_map'
+        #else:
+            --gene_trans_map 'none'
+        #end if
+
         #for $entry in $samples:
             '${re.sub('[^\w\-_]', '_', entry.element_identifier)}'
         #end for
+
+        && mv *.isoform.counts.matrix '$trans_counts'
+        && mv *.isoform.TPM.not_cross_norm '$TPM_no_norm'
+        #if $gene_trans_map:
+            && mv *.gene.counts.matrix '$trans_counts_gene'
+            && mv *.gene.TPM.not_cross_norm '$TPM_no_norm_gene'
+        #end if
+
+        #if $additional_params.cross_sample_norm == "TMM":
+            && mv *.isoform.TMM.EXPR.matrix '$norm_TMM'
+            #if $gene_trans_map:
+                && mv *.gene.TMM.EXPR.matrix '$norm_TMM_gene'
+            #end if
+        #else if $additional_params.cross_sample_norm == "UpperQuartile":
+            && mv *.isoform.UpperQuartile.EXPR.matrix '$norm_UQ'
+            #if $gene_trans_map:
+                && mv *.gene.UpperQuartile.EXPR.matrix '$norm_UQ_gene'
+            #end if
+        #end if
     ]]></command>
     <inputs>
         <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" />
-
+        <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" optional="true" help="Only needed for gene level estimates" />
         <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
             <option value="RSEM">RSEM</option>
             <option value="eXpress">eXpress</option>
@@ -42,14 +67,29 @@
         </section>
     </inputs>
     <outputs>
-        <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment counts (raw counts)" from_work_dir="matrix.counts.matrix"/>
-        <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of TPM expression values (not cross-sample normalized)" from_work_dir="matrix.TPM.not_cross_norm"/>
-        <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values" from_work_dir="matrix.TMM.EXPR.matrix">
+        <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment isoform counts (raw counts)"/>
+        <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of isoform TPM expression values (not cross-sample normalized)"/>
+
+        <data format="tabular" name="trans_counts_gene" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment gene counts (raw counts)">
+            <filter>gene_trans_map</filter>
+        </data>
+        <data format="tabular" name="TPM_no_norm_gene" label="${tool.name} on ${on_string}: matrix of gene TPM expression values (not cross-sample normalized)">
+            <filter>gene_trans_map</filter>
+        </data>
+
+        <data format="tabular" name="norm_TMM" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values">
             <filter>additional_params['cross_sample_norm'] == "TMM"</filter>
         </data>
-        <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values" from_work_dir="matrix.UpperQuartile.EXPR.matrix">
+        <data format="tabular" name="norm_UQ" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values">
             <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter>
         </data>
+
+        <data format="tabular" name="norm_TMM_gene" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values">
+            <filter>additional_params['cross_sample_norm'] == "TMM" and gene_trans_map</filter>
+        </data>
+        <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values">
+            <filter>additional_params['cross_sample_norm'] == "UpperQuartile" and gene_trans_map</filter>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -68,7 +108,7 @@
                     <has_n_columns n="3" />
                 </assert_contents>
             </output>
-            <output name="norm">
+            <output name="norm_TMM">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
                     <has_n_columns n="3" />
@@ -91,7 +131,7 @@
                     <has_n_columns n="3" />
                 </assert_contents>
             </output>
-            <output name="norm">
+            <output name="norm_TMM">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
                     <has_n_columns n="3" />
@@ -114,7 +154,7 @@
                     <has_n_columns n="3" />
                 </assert_contents>
             </output>
-            <output name="norm">
+            <output name="norm_TMM">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
                     <has_n_columns n="3" />
@@ -137,7 +177,7 @@
                     <has_n_columns n="3" />
                 </assert_contents>
             </output>
-            <output name="norm">
+            <output name="norm_UQ">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
                 </assert_contents>
@@ -193,7 +233,7 @@
                     <has_n_columns n="3" />
                 </assert_contents>
             </output>
-            <output name="norm">
+            <output name="norm_TMM">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
                     <has_n_columns n="3" />