diff salmonquant.xml @ 19:accd772edf70 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664

--- a/salmonquant.xml	Thu Jul 22 14:02:44 2021 +0000
+++ b/salmonquant.xml	Wed Dec 07 19:30:24 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="salmon" name="Salmon quant" version="@VERSION@+@GALAXY_VERSION@" profile="@PROFILE_VERSION@">
+<tool id="salmon" name="Salmon quant" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">
     <description>Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads</description>
     <macros>
         <import>macros.xml</import>
@@ -12,7 +12,7 @@
             @salalign@
         #end if
         @salquant@
-        #if $quant_type.qtype == "reads" and $quant_type.writeMappings:
+        #if $quant_type.qtype == "reads" and $quant_type.bam_options.writeMappings:
             && @bam_sort@ ./output/samout.sam
         #end if
         #if $quant_type.qtype == "alignment" and $quant_type.sampleOut:
@@ -37,14 +37,14 @@
         <expand macro="quantboth"/>
     </inputs>
     <outputs>
-        <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
-        <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
+        <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string}: transcript quantification" />
+        <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string}: gene quantification">
             <filter>geneMap</filter>
         </data>
-        <data name="output_bam" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string} (BAM format)">
-            <filter>quant_type['qtype'] == "reads" and quant_type['writeMappings']</filter>
+        <data name="output_bam" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string}: BAM">
+            <filter>quant_type['qtype'] == "reads" and quant_type['bam_options']['writeMappings']</filter>
         </data>
-        <data name="postSample" format="bam" from_work_dir="output/bamout.bam" label="Sampled input alignments on ${on_string}(BAM format)">
+        <data name="postSample" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string}: sampled input alignments">
             <filter>quant_type['qtype'] == "alignment" and quant_type['sampleOut']</filter>
         </data>
     </outputs>
@@ -68,7 +68,9 @@
                         </conditional>
                     </conditional>
                 </section>
-                <param name="writeMappings" value="true"/>
+                <conditional name="bam_options">
+                    <param name="writeMappings" value="--writeMappings=./output/samout.sam"/>
+                </conditional>
             </conditional>
             <output name="output_quant" ftype="tabular">
                 <assert_contents>
@@ -102,7 +104,9 @@
                     <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />
                     <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />
                 </section>
-                <param name="writeMappings" value="true"/>
+                <conditional name="bam_options">
+                    <param name="writeMappings" value="--writeMappings=./output/samout.sam"/>
+                </conditional>            
             </conditional>
             <output name="output_quant" ftype="tabular">
                 <assert_contents>
@@ -183,6 +187,7 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Test 05 -->
         <test expect_num_outputs="2">
             <conditional name="quant_type">
                 <param name="qtype" value="alignment"/>
@@ -315,6 +320,89 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Test 10 -->
+        <!-- Test writeQualities option-->
+        <test expect_num_outputs="2">
+            <conditional name="quant_type">
+                <param name="qtype" value="reads"/>
+                <conditional name="refTranscriptSource">
+                    <param name="TranscriptSource" value="history"/>
+                    <section name="s_index">
+                        <param name="fasta" value="transcripts.fasta"/>
+                    </section>
+                </conditional>
+                <section name="input">
+                    <param name="single_or_paired.single_or_paired_opts" value="paired" />
+                    <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />
+                    <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />
+                </section>
+                <conditional name="bam_options">
+                    <param name="writeMappings" value="--writeMappings=./output/samout.sam"/>
+                    <param name="writeQualities" value="true"/>
+                </conditional>            
+            </conditional>
+            <output name="output_quant" ftype="tabular">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="--libType A"/>
+            </assert_command>
+        </test>
+        <!-- Test genome input for decoy index -->
+        <test expect_num_outputs="2">
+            <conditional name="quant_type">
+                <param name="qtype" value="reads"/>
+                <conditional name="refTranscriptSource">
+                    <param name="TranscriptSource" value="history"/>
+                    <section name="s_index">
+                        <param name="fasta" value="transcripts.fasta"/>
+                        <param name="genome" value="genome.fasta"/>
+                    </section>
+                </conditional>
+                <section name="input">
+                    <conditional name="single_or_paired">
+                        <param name="single_or_paired_opts" value="paired" />
+                        <param name="input_mate1" value="fastqs/reads_1.fastq" />
+                        <param name="input_mate2" value="fastqs/reads_2.fastq" />
+                        <conditional name="libtype">
+                            <param name="strandedness" value="U"/>
+                        </conditional>
+                    </conditional>
+                </section>
+                <conditional name="bam_options">
+                    <param name="writeMappings" value="--writeMappings=./output/samout.sam"/>
+                </conditional>
+            </conditional>
+            <output name="output_quant" ftype="tabular">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="--libType IU"/>
+                <has_text text="--decoy"/>
+            </assert_command>
+        </test>
     </tests>
     <help><![CDATA[
         @salmonhelp@