Add minimal wrapper for minia

tools/minia/.shed.yml

@@ -0,0 +1,11 @@
+categories:
+- Assembly
+description: Short-read assembler based on a de Bruijn graph
+long_description: |
+  Minia is capable of assembling a human genome on a desktop computer in a day.
+  The output of Minia is a set of contigs.
+name: minia
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia
+homepage_url: https://gatb.inria.fr/software/minia/
+type: unrestricted

tools/minia/minia.xml

@@ -0,0 +1,55 @@
+<tool id="minia" name="Minia" version="@TOOL_VERSION@">
+    <description>Short-read assembler based on a de Bruijn graph</description>
+    <macros>
+        <token name="@TOOL_VERSION@">3.2.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">minia</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+#set input = 'infile.' + $in.ext
+ln -s '$in' '$input' &&
+
+minia
+-in '$input'
+-kmer-size $kmer_size
+#if str($abundance_min):
+    -abundance-min $abundance_min
+#end if
+#if str($abundance_max):
+    -abundance-min $abundance_max
+#end if
+-nb-cores \${GALAXY_SLOTS:-1}
+-out output
+    ]]></command>
+    <inputs>
+        <param argument="-in" type="data" format="fasta,fastqsanger,fastqsanger.gz,fasta.gz" label="Reads in FASTA or FASTQ format" />
+        <param argument="-kmer-size" type="integer" value="31" min="1" label="Size of a kmer" />
+        <param argument="-abundance-min" type="integer" value="" optional="true" min="0" label="Min abundance threshold for solid kmers (default: 2)" />
+        <param argument="-abundance-max" type="integer" value="" optional="true" label="Max abundance threshold for solid kmers" />
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta" label="${tool.name} on ${on_string}" from_work_dir="output.contigs.fa" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="in" value="ec.fa" />
+            <param name="kmer_size" value="21" />
+            <param name="abundance_min" value="1" />
+            <output name="output" ftype="fasta">
+                <assert_contents>
+                    <has_text text="LN:i:460 KC:i:2200 km:f:5.000"/>
+                    <has_text text="LN:i:637 KC:i:3085 km:f:5.000"/>
+                    <has_n_lines n="4"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.
+The output of Minia is a set of contigs.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1186/1748-7188-8-22</citation>
+    </citations>
+</tool>

tools/minia/test-data/ec.fa

@@ -0,0 +1,49 @@
+>works well for k=21; part of genome10K.fasta
+CATCGATGCGAGACGCCTGTCGCGGGGAATTGTGGGGCGGACCACGCTCTGGCTAACGAGCTACCGTTTCCTTTAACCTGCCAGACGGTGACCAGGGCCGTTCGGCGTTGCATCGAGCGGTGTCGCTAGCGCAATGCGCAAGATTTTGACATTTACAAGGCAACATTGCAGCGTCCGATGGTCCGGTGGCCTCCAGATAGTGTCCAGTCGCTCTAACTGTATGGAGACCATAGGCATTTACCTTATTCTCATCGCCACGCCCCAAGATCTTTAGGACCCAGCATTCCTTTAACCACTAACATAACGCGTGTCATCTAGTTCAACAACC
+>remaining part
+TGTCATCTAGTTCAACAACCGTTATGCCGTCCGACTCTTGCGCTCGGATGTCCGCAATGGGTTATCCCTATGTTCCGGTAATCTCTCATCTACTAAGCGCCCTAAAGGTCGTATGGTTGGAGGGCGGTTACACACCCTTAAGTACCGAACGATAGAGCACCCGTCTAGGAGGGCGTGCAGGGTCTCCCGCTAGCTAATGGTCACGGCCTCTCTGGGAAAGCTGAACAACGGATGATACCCATACTGCCACTCCAGTACCTGGGCCGCGTGTTGTACGCTGTGTATCTTGAGAGCGTTTCCAGCAGATAGAACAGGATCACATGTACATG
+>that's the EC
+TGTCATCTAGTTCAACAACCAAAAAAA
+>contig that is split in two by the EC, containing the last kmer of the ec (CTAGTTCAACAACCAAAAAAA)
+GGTGAACAGCACATCTTTTCGTCCTGAGGCCATATTAATTCTACTCAGATTGTCTGTAACCGGAGCTTCGGGCGTATTTTTGCGTAAGACACTGCCTAAAGGGAACATATGTGTCCAGAATAGGGTTCAACGGTGTATGAGCAAA
+CTAGTTCAACAACCAAAAAAA
+TTGTGTGCAAGCTACTTCTAGACCTTATTAAGTGCCCAGGAATTCCTAGGAAGGCGCGCAGCTCAAGCAATCATACATGGCGGAATGCCTGTCCACCGGGGGTTCTACTGTACCACAGTGGCCTGGATAGCTAAGCAGGTCCTGGATTGGCATGTCATCCGGAGTGATAGGCACTGCTCACGACCAGCTTGCGGACAAACGGGGTGCCCGCGCCTGCGTCCGGTAGACGAGCGATGGATTTAGACCGTTCACTGAACCCTCTAATAGGACCTCTTGCCCATCCGAGGCTTAAGC
+>the rest below is just repeated for coverage reasons
+A
+>the rest below is just repeated for coverage reasons
+A
+>the rest below is just repeated for coverage reasons
+A
+>contig that is split in two by the EC, containing the last kmer of the ec (CTAGTTCAACAACCAAAAAAA)
+GGTGAACAGCACATCTTTTCGTCCTGAGGCCATATTAATTCTACTCAGATTGTCTGTAACCGGAGCTTCGGGCGTATTTTTGCGTAAGACACTGCCTAAAGGGAACATATGTGTCCAGAATAGGGTTCAACGGTGTATGAGCAAA
+CTAGTTCAACAACCAAAAAAA
+TTGTGTGCAAGCTACTTCTAGACCTTATTAAGTGCCCAGGAATTCCTAGGAAGGCGCGCAGCTCAAGCAATCATACATGGCGGAATGCCTGTCCACCGGGGGTTCTACTGTACCACAGTGGCCTGGATAGCTAAGCAGGTCCTGGATTGGCATGTCATCCGGAGTGATAGGCACTGCTCACGACCAGCTTGCGGACAAACGGGGTGCCCGCGCCTGCGTCCGGTAGACGAGCGATGGATTTAGACCGTTCACTGAACCCTCTAATAGGACCTCTTGCCCATCCGAGGCTTAAGC
+>contig that is split in two by the EC, containing the last kmer of the ec (CTAGTTCAACAACCAAAAAAA)
+GGTGAACAGCACATCTTTTCGTCCTGAGGCCATATTAATTCTACTCAGATTGTCTGTAACCGGAGCTTCGGGCGTATTTTTGCGTAAGACACTGCCTAAAGGGAACATATGTGTCCAGAATAGGGTTCAACGGTGTATGAGCAAA
+CTAGTTCAACAACCAAAAAAA
+TTGTGTGCAAGCTACTTCTAGACCTTATTAAGTGCCCAGGAATTCCTAGGAAGGCGCGCAGCTCAAGCAATCATACATGGCGGAATGCCTGTCCACCGGGGGTTCTACTGTACCACAGTGGCCTGGATAGCTAAGCAGGTCCTGGATTGGCATGTCATCCGGAGTGATAGGCACTGCTCACGACCAGCTTGCGGACAAACGGGGTGCCCGCGCCTGCGTCCGGTAGACGAGCGATGGATTTAGACCGTTCACTGAACCCTCTAATAGGACCTCTTGCCCATCCGAGGCTTAAGC
+>works well for k=21; part of genome10K.fasta
+CATCGATGCGAGACGCCTGTCGCGGGGAATTGTGGGGCGGACCACGCTCTGGCTAACGAGCTACCGTTTCCTTTAACCTGCCAGACGGTGACCAGGGCCGTTCGGCGTTGCATCGAGCGGTGTCGCTAGCGCAATGCGCAAGATTTTGACATTTACAAGGCAACATTGCAGCGTCCGATGGTCCGGTGGCCTCCAGATAGTGTCCAGTCGCTCTAACTGTATGGAGACCATAGGCATTTACCTTATTCTCATCGCCACGCCCCAAGATCTTTAGGACCCAGCATTCCTTTAACCACTAACATAACGCGTGTCATCTAGTTCAACAACC
+>remaining part
+TGTCATCTAGTTCAACAACCGTTATGCCGTCCGACTCTTGCGCTCGGATGTCCGCAATGGGTTATCCCTATGTTCCGGTAATCTCTCATCTACTAAGCGCCCTAAAGGTCGTATGGTTGGAGGGCGGTTACACACCCTTAAGTACCGAACGATAGAGCACCCGTCTAGGAGGGCGTGCAGGGTCTCCCGCTAGCTAATGGTCACGGCCTCTCTGGGAAAGCTGAACAACGGATGATACCCATACTGCCACTCCAGTACCTGGGCCGCGTGTTGTACGCTGTGTATCTTGAGAGCGTTTCCAGCAGATAGAACAGGATCACATGTACATG
+>works well for k=21; part of genome10K.fasta
+CATCGATGCGAGACGCCTGTCGCGGGGAATTGTGGGGCGGACCACGCTCTGGCTAACGAGCTACCGTTTCCTTTAACCTGCCAGACGGTGACCAGGGCCGTTCGGCGTTGCATCGAGCGGTGTCGCTAGCGCAATGCGCAAGATTTTGACATTTACAAGGCAACATTGCAGCGTCCGATGGTCCGGTGGCCTCCAGATAGTGTCCAGTCGCTCTAACTGTATGGAGACCATAGGCATTTACCTTATTCTCATCGCCACGCCCCAAGATCTTTAGGACCCAGCATTCCTTTAACCACTAACATAACGCGTGTCATCTAGTTCAACAACC
+>remaining part
+TGTCATCTAGTTCAACAACCGTTATGCCGTCCGACTCTTGCGCTCGGATGTCCGCAATGGGTTATCCCTATGTTCCGGTAATCTCTCATCTACTAAGCGCCCTAAAGGTCGTATGGTTGGAGGGCGGTTACACACCCTTAAGTACCGAACGATAGAGCACCCGTCTAGGAGGGCGTGCAGGGTCTCCCGCTAGCTAATGGTCACGGCCTCTCTGGGAAAGCTGAACAACGGATGATACCCATACTGCCACTCCAGTACCTGGGCCGCGTGTTGTACGCTGTGTATCTTGAGAGCGTTTCCAGCAGATAGAACAGGATCACATGTACATG
+>contig that is split in two by the EC, containing the last kmer of the ec (CTAGTTCAACAACCAAAAAAA)
+GGTGAACAGCACATCTTTTCGTCCTGAGGCCATATTAATTCTACTCAGATTGTCTGTAACCGGAGCTTCGGGCGTATTTTTGCGTAAGACACTGCCTAAAGGGAACATATGTGTCCAGAATAGGGTTCAACGGTGTATGAGCAAA
+CTAGTTCAACAACCAAAAAAA
+TTGTGTGCAAGCTACTTCTAGACCTTATTAAGTGCCCAGGAATTCCTAGGAAGGCGCGCAGCTCAAGCAATCATACATGGCGGAATGCCTGTCCACCGGGGGTTCTACTGTACCACAGTGGCCTGGATAGCTAAGCAGGTCCTGGATTGGCATGTCATCCGGAGTGATAGGCACTGCTCACGACCAGCTTGCGGACAAACGGGGTGCCCGCGCCTGCGTCCGGTAGACGAGCGATGGATTTAGACCGTTCACTGAACCCTCTAATAGGACCTCTTGCCCATCCGAGGCTTAAGC
+>contig that is split in two by the EC, containing the last kmer of the ec (CTAGTTCAACAACCAAAAAAA)
+GGTGAACAGCACATCTTTTCGTCCTGAGGCCATATTAATTCTACTCAGATTGTCTGTAACCGGAGCTTCGGGCGTATTTTTGCGTAAGACACTGCCTAAAGGGAACATATGTGTCCAGAATAGGGTTCAACGGTGTATGAGCAAA
+CTAGTTCAACAACCAAAAAAA
+TTGTGTGCAAGCTACTTCTAGACCTTATTAAGTGCCCAGGAATTCCTAGGAAGGCGCGCAGCTCAAGCAATCATACATGGCGGAATGCCTGTCCACCGGGGGTTCTACTGTACCACAGTGGCCTGGATAGCTAAGCAGGTCCTGGATTGGCATGTCATCCGGAGTGATAGGCACTGCTCACGACCAGCTTGCGGACAAACGGGGTGCCCGCGCCTGCGTCCGGTAGACGAGCGATGGATTTAGACCGTTCACTGAACCCTCTAATAGGACCTCTTGCCCATCCGAGGCTTAAGC
+>works well for k=21; part of genome10K.fasta
+CATCGATGCGAGACGCCTGTCGCGGGGAATTGTGGGGCGGACCACGCTCTGGCTAACGAGCTACCGTTTCCTTTAACCTGCCAGACGGTGACCAGGGCCGTTCGGCGTTGCATCGAGCGGTGTCGCTAGCGCAATGCGCAAGATTTTGACATTTACAAGGCAACATTGCAGCGTCCGATGGTCCGGTGGCCTCCAGATAGTGTCCAGTCGCTCTAACTGTATGGAGACCATAGGCATTTACCTTATTCTCATCGCCACGCCCCAAGATCTTTAGGACCCAGCATTCCTTTAACCACTAACATAACGCGTGTCATCTAGTTCAACAACC
+>remaining part
+TGTCATCTAGTTCAACAACCGTTATGCCGTCCGACTCTTGCGCTCGGATGTCCGCAATGGGTTATCCCTATGTTCCGGTAATCTCTCATCTACTAAGCGCCCTAAAGGTCGTATGGTTGGAGGGCGGTTACACACCCTTAAGTACCGAACGATAGAGCACCCGTCTAGGAGGGCGTGCAGGGTCTCCCGCTAGCTAATGGTCACGGCCTCTCTGGGAAAGCTGAACAACGGATGATACCCATACTGCCACTCCAGTACCTGGGCCGCGTGTTGTACGCTGTGTATCTTGAGAGCGTTTCCAGCAGATAGAACAGGATCACATGTACATG
+>works well for k=21; part of genome10K.fasta
+CATCGATGCGAGACGCCTGTCGCGGGGAATTGTGGGGCGGACCACGCTCTGGCTAACGAGCTACCGTTTCCTTTAACCTGCCAGACGGTGACCAGGGCCGTTCGGCGTTGCATCGAGCGGTGTCGCTAGCGCAATGCGCAAGATTTTGACATTTACAAGGCAACATTGCAGCGTCCGATGGTCCGGTGGCCTCCAGATAGTGTCCAGTCGCTCTAACTGTATGGAGACCATAGGCATTTACCTTATTCTCATCGCCACGCCCCAAGATCTTTAGGACCCAGCATTCCTTTAACCACTAACATAACGCGTGTCATCTAGTTCAACAACC
+>remaining part
+TGTCATCTAGTTCAACAACCGTTATGCCGTCCGACTCTTGCGCTCGGATGTCCGCAATGGGTTATCCCTATGTTCCGGTAATCTCTCATCTACTAAGCGCCCTAAAGGTCGTATGGTTGGAGGGCGGTTACACACCCTTAAGTACCGAACGATAGAGCACCCGTCTAGGAGGGCGTGCAGGGTCTCCCGCTAGCTAATGGTCACGGCCTCTCTGGGAAAGCTGAACAACGGATGATACCCATACTGCCACTCCAGTACCTGGGCCGCGTGTTGTACGCTGTGTATCTTGAGAGCGTTTCCAGCAGATAGAACAGGATCACATGTACATG
+

tools/odgi/build.xml

@@ -23,8 +23,8 @@ $sort
             help="" />
     </inputs>
     <outputs>
-        <data name="odgi_output" format="odgi" />
-        <data name="gfa_output" format="gfa1">
+        <data name="odgi_output" format="odgi" label="${tool.name} on ${on_string}: odgi" />
+        <data name="gfa_output" format="gfa1" label="${tool.name} on ${on_string}: GFA">
             <filter>to_gfa</filter>
         </data>
     </outputs>

tools/odgi/vis.xml

@@ -37,7 +37,7 @@ $path_per_row
             label="Show thin links of this relative width to connect path pieces" />
     </inputs>
     <outputs>
-        <data name="output" format="png" />
+        <data name="output" format="png" label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
         <test>