# HG changeset patch
# User bgruening
# Date 1710754569 0
# Node ID c9944a2600f1e550370b62cfdb4245856d6451e9
# Parent  e32b215b7c043dc2e939a29b767e6d7085fea097
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a

diff -r e32b215b7c04 -r c9944a2600f1 alevin.xml
--- a/alevin.xml	Fri Jun 23 17:03:24 2023 +0000
+++ b/alevin.xml	Mon Mar 18 09:36:09 2024 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         mkdir ./index
@@ -269,7 +270,13 @@
                 <param name="freqThreshold" value="5"/>
                 <param name="dumpMtx" value="true"/>
             </section>
-            <output name="quants_mat_mtx" file="alevin_mat_01.mtx" ftype="mtx" sort="true"/>
+            <output name="quants_mat_mtx" file="alevin_mat_01.mtx" compare="sim_size" ftype="mtx">
+                <assert_contents>
+                    <has_text text="MatrixMarket" />
+                    <has_n_columns n="5" />
+                    <has_n_lines n="105" />
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="11">
             <conditional name="refTranscriptSource">
@@ -296,7 +303,13 @@
                 <param name="freqThreshold" value="5"/>
                 <param name="dumpMtx" value="true"/>
             </section>
-            <output name="quants_mat_mtx" file="alevin_mat_02.mtx" ftype="mtx" sort="true"/>
+            <output name="quants_mat_mtx" file="alevin_mat_02.mtx" compare="sim_size" ftype="mtx" >
+                <assert_contents>
+                    <has_text text="MatrixMarket" />
+                    <has_n_columns n="5" />
+                    <has_n_lines n="105" />
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="8">
             <conditional name="refTranscriptSource">
@@ -323,7 +336,13 @@
                 <param name="freqThreshold" value="5"/>
                 <param name="dumpMtx" value="true"/>
             </section>
-            <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx" ftype="mtx" sort="true"/>
+            <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx"  compare="sim_size" ftype="mtx">
+                <assert_contents>
+                    <has_text text="MatrixMarket" />
+                    <has_n_columns n="5" />
+                    <has_n_lines n="105" />
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="14">
             <conditional name="refTranscriptSource">
@@ -347,7 +366,13 @@
             <section name="optional">
                 <param name="dumpMtx" value="true"/>
             </section>
-            <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true"/>
+            <output name="quants_mat_mtx" file="alevin_mat.mtx"  compare="sim_size" ftype="mtx">
+                <assert_contents>
+                    <has_text text="MatrixMarket" />
+                    <has_n_columns n="5" />
+                    <has_n_lines n="17" />
+                </assert_contents>
+            </output>
             <output name="salmon_quant_log" ftype="txt">
                 <assert_contents>
                     <has_text text="Index contained 322 targets"/>
@@ -363,7 +388,7 @@
             <output_collection name="umigraphs" type="list" count="14">
                 <element name="AGTGGGATCTTAACCT">
                     <assert_contents>
-                        <has_size value="4017" delta="1000"/>
+                        <has_size value="4661" delta="1000"/>
                     </assert_contents>
                 </element>
             </output_collection>
diff -r e32b215b7c04 -r c9944a2600f1 macros.xml
--- a/macros.xml	Fri Jun 23 17:03:24 2023 +0000
+++ b/macros.xml	Mon Mar 18 09:36:09 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: