diff salmonquant.xml @ 18:c6c81a918ae1 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"

--- a/salmonquant.xml	Sat Oct 03 18:20:44 2020 +0000
+++ b/salmonquant.xml	Thu Jul 22 14:02:44 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="salmon" name="Salmon quant" version="@VERSION@+galaxy1">
+<tool id="salmon" name="Salmon quant" version="@VERSION@+@GALAXY_VERSION@" 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>
@@ -59,10 +59,14 @@
                     </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" />
-                    <param name="single_or_paired.strandedness" value="U"/>
+                    <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>
                 <param name="writeMappings" value="true"/>
             </conditional>
@@ -80,6 +84,43 @@
                     <has_n_columns n="5" />
                 </assert_contents>
             </output>
+            <assert_command>
+                <has_text text="--libType IU"/>
+            </assert_command>
+        </test>
+        <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>
+                <param name="writeMappings" value="true"/>
+            </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 expect_num_outputs="1">
             <conditional name="quant_type">
@@ -152,11 +193,30 @@
                 <param name="noErrorModel" value="--noErrorModel"/>
                 <param name="numErrorBins" value="5"/>
             </conditional>
-            <output name="postSample" ftype="bam" value="postSample.bam"/>
+            <!-- bam output uses non-deterministic sampling, so can only use compare="sim_size" -->
+            <output name="postSample" ftype="bam" value="postSample.bam" compare="sim_size" delta="20000"/>
             <assert_stderr>
                 <has_text text="Sampling alignments; outputting results to ./output/postSample.bam"/>
             </assert_stderr>
         </test>
+        <test expect_num_outputs="2">
+            <conditional name="quant_type">
+                <param name="qtype" value="alignment"/>
+                <param name="afile" value="salmonbam.bam"/>
+                <param name="ont" value="true" />
+                <param name="transcript" value="transcripts.fasta"/>
+                <param name="sampleOut" value="--sampleOut"/>
+                <param name="sampleUnaligned" value="--sampleUnaligned"/>
+                <param name="noErrorModel" value="--noErrorModel"/>
+                <param name="numErrorBins" value="5"/>
+            </conditional>
+            <assert_stderr>
+                <has_text text="Sampling alignments; outputting results to ./output/postSample.bam"/>
+            </assert_stderr>
+            <assert_command>
+                <has_text text=" --ont "/>
+            </assert_command>
+        </test>
         <test expect_num_outputs="1">
             <conditional name="quant_type">
                 <param name="qtype" value="reads"/>