changeset 20:f4d5237a84f6 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a

--- a/macros.xml	Fri Jun 23 17:02:35 2023 +0000
+++ b/macros.xml	Mon Mar 18 09:35:41 2024 +0000
@@ -1,8 +1,13 @@
 <macros>
     <token name="@TOOL_VERSION@">1.10.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@IDX_VERSION@">q7</token>
     <token name="@PROFILE_VERSION@">20.01</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">salmon</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
@@ -121,9 +126,10 @@
         label="Discard orphan quasi"
         help="Discard orphan mappings in quasi-mapping mode. If this flag is passed then only paired mappings will be considered toward quantification estimates.  The default behavior is to consider orphan mappings if no valid paired mappings exist."/>
         <conditional name="validmap">
-            <param name="validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False"
-            label="Validate mappings"
-            help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification."/>
+            <param name="validateMappings" type="select" label="Validate mappings" help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification.">
+                <option value="--validateMappings">True</option>
+                <option value="" selected="true">False</option>
+            </param>
             <when value="--validateMappings">
                 <param name="minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
                 label="Min Score Fraction"
@@ -390,7 +396,7 @@
             #end if
             ln -s '${quant_type.input.single_or_paired.input_1.forward}' ./mate1.$ext &&
             ln -s '${quant_type.input.single_or_paired.input_1.reverse}' ./mate2.$ext &&
-        #else if '$quant_type.input.single_or_paired.single_or_paired_opts' == 'paired_interleaved':
+        #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_interleaved':
             #if $quant_type.input.single_or_paired.input_1.ext == 'fasta':
                 #set $ext = 'fasta'
             #else:

--- a/salmonquant.xml	Fri Jun 23 17:02:35 2023 +0000
+++ b/salmonquant.xml	Mon Mar 18 09:35:41 2024 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <command detect_errors="aggressive"><![CDATA[
         #if $quant_type.qtype == "reads":
@@ -403,6 +404,47 @@
                 <has_text text="--decoy"/>
             </assert_command>
         </test>
+        <!-- test 12: interleaved input -->
+        <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">
+                    <conditional name="single_or_paired">
+                        <param name="single_or_paired_opts" value="paired_interleaved" />
+                        <param name="input_1" value="fastqs/reads_both.fastq.bz2" />
+                        <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"/>
+            </assert_command>
+        </test>
     </tests>
     <help><![CDATA[
         @salmonhelp@