diff alevin.xml @ 14:c9944a2600f1 draft

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

--- 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>