diff pangolin.xml @ 3:514a786baaa9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"

--- a/pangolin.xml	Sun Apr 25 20:46:03 2021 +0000
+++ b/pangolin.xml	Wed May 19 13:32:34 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@" profile="20.01">
+<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01">
     <description>Phylogenetic Assignment of Outbreak Lineages</description>
     <macros>
         <token name="@TOOL_VERSION@">2.3.8</token>
@@ -23,20 +23,26 @@
         --max-ambig $max_ambig
         --min-length $min_length
         '$input1'
-        && csvtk csv2tab report.csv | tail -n-1 >'$output1'
+        && csvtk csv2tab report.csv
+        #if not $include_header:
+            | tail -n+2 
+        #end if
+        > '$output1'
         #if $alignment
             && mv sequences.aln.fasta '$align1'
         #end if 
     ]]></command>
     <inputs>
-      <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" /> 
-      <param name="alignment" type="boolean" label="Generate output alignment" 
+        <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" /> 
+        <param name="alignment" type="boolean" label="Generate output alignment" 
             truevalue="--alignment" falsevalue="" /> 
-      <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed" 
-          value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" />
-      <param argument="--min-length" type="integer" label="Minimum query length allowed" 
-          value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>
-      <conditional name="db">
+        <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed" 
+            value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" />
+        <param argument="--min-length" type="integer" label="Minimum query length allowed" 
+            value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>
+        <param name="include_header" type="boolean" label="Include header line in output file" 
+            truevalue="true" falsevalue="false" />
+        <conditional name="db">
             <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database">
                 <option value="download">Download latest from web</option>
                 <option value="builtin">Use database from Galaxy server</option>
@@ -49,7 +55,7 @@
                     <options from_data_table="pangolearn">
                         <column name="value" index="0" />
                         <column name="name" index="1" />
-                        <column name="path" index="3" />                         
+                        <column name="path" index="3" />
                         <filter type="sort_by" column="0"/>
                     </options>
                 </param>
@@ -69,43 +75,83 @@
         </data>
     </outputs>
     <tests>
-      <test expect_num_outputs="1">
-          <param name="input1" value="test1.fasta"/>
-          <conditional name="db">
-              <param name="source" value="download" />
-          </conditional>
-          <output name="output1">
-            <assert_contents>
-                <has_text text="B.1.1" />
-                <has_text text="passed_qc" />
-            </assert_contents>
-          </output>
-      </test>
-      <test expect_num_outputs="2">
-          <param name="alignment" value="--alignment" />
-          <param name="input1" value="test1.fasta" />
-          <conditional name="db">
-            <param name="source" value="download" />
-          </conditional>
-          <output name="output1">
-            <assert_contents>
-                <has_text text="B.1.1" />
-                <has_text text="passed_qc" />
-            </assert_contents>
-          </output>
-          <output name="align1" file="aln1.fasta" ftype="fasta" />
-      </test>
-      <test expect_num_outputs="1">
-        <param name="input1" value="test1.fasta"/>
-        <conditional name="db">
-            <param name="source" value="builtin" />
-        </conditional>
-        <output name="output1">
-            <assert_contents>
-                <has_text text="2021-04-21" />
-            </assert_contents>
-        </output>
-    </test>
+        <test expect_num_outputs="1">
+            <param name="input1" value="test1.fasta"/>
+            <conditional name="db">
+                <param name="source" value="download" />
+            </conditional>
+            <output name="output1" ftype="tabular">
+                <assert_contents>
+                    <has_text text="B.1.1" />
+                    <has_text text="passed_qc" />
+                    <has_n_lines n="1" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="alignment" value="--alignment" />
+            <param name="input1" value="test1.fasta" />
+            <conditional name="db">
+                <param name="source" value="download" />
+            </conditional>
+            <output name="output1" ftype="tabular">
+                <assert_contents>
+                    <has_text text="B.1.1" />
+                    <has_text text="passed_qc" />
+                    <has_n_lines n="1" />
+                </assert_contents>
+            </output>
+            <output name="align1" file="aln1.fasta" ftype="fasta">
+                <assert_contents>
+                    <has_text text="Consensus_EB232-crude-prep_S297" />
+                    <has_n_lines n="2" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input1" value="test1.fasta"/>
+            <conditional name="db">
+                <param name="source" value="builtin" />
+            </conditional>
+            <output name="output1" ftype="tabular">
+                <assert_contents>
+                    <has_text text="Consensus_EB232-crude-prep_S297" />
+                    <has_n_lines n="1" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input1" value="multiple_alignment.fasta.gz"/>
+            <conditional name="db">
+                <param name="source" value="builtin" />
+            </conditional>
+            <output name="output1" ftype="tabular">
+                <assert_contents>
+                    <has_text text="Serbia" />
+                    <has_text text="Poland" />
+                    <has_text text="USA" />
+                    <has_n_lines n="34" />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- test include-header option -->
+        <test expect_num_outputs="1">
+            <param name="input1" value="multiple_alignment.fasta.gz"/>
+            <param name="include_header" value="true" />
+            <conditional name="db">
+                <param name="source" value="builtin" />
+            </conditional>
+            <output name="output1" ftype="tabular">
+                <assert_contents>
+                    <has_text text="pangoLEARN_version" />
+                    <has_text text="lineage" />
+                    <has_text text="Serbia" />
+                    <has_text text="Poland" />
+                    <has_text text="USA" />
+                    <has_n_lines n="35" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[