fix case where no samples were lost

ErasmusMC-Bioinformatics · Jan 29, 2019 · 05c2770 · 05c2770
1 parent 33213e4
commit 05c2770
Showing 1 changed file with 16 additions and 7 deletions.
diff --git a/tools/mycrobiota/recover_samples_discarded_by_subsample.xml b/tools/mycrobiota/recover_samples_discarded_by_subsample.xml
@@ -19,17 +19,17 @@
         &&
         if [ -z "\$samples"];
             then
-                touch fasta.pick.dat;
-                touch group.pick.dat;
+                cp fasta2.dat final_fasta;
+                cp group2.dat final_group;
             else
                 echo "get.groups(fasta=fasta.dat, group=group.dat, groups=\$samples)" | sed 's/ //g' | mothur;
-        fi
 
-        ## merge selected reads (fasta.pick.dat) with the fasta file from after sub.sample
-        && echo "merge.files(input=fasta2.dat-fasta.pick.dat, output=final_fasta)" | sed 's/ //g' | mothur
+                ## merge selected reads (fasta.pick.dat) with the fasta file from after sub.sample
+                echo "merge.files(input=fasta2.dat-fasta.pick.dat, output=final_fasta)" | sed 's/ //g' | mothur;
 
-        ## merge group files
-        && echo "merge.files(input=group2.dat-group.pick.dat, output=final_group)" | sed 's/ //g' | mothur
+                ## merge group files
+                echo "merge.files(input=group2.dat-group.pick.dat, output=final_group)" | sed 's/ //g' | mothur;
+        fi
 
     ]]></command>
     <inputs>
@@ -53,6 +53,15 @@
             <output name="out_fasta" file="recovered.fasta"/>
             <output name="out_group" file="recovered.groups"/>
         </test>
+        <test><!-- test case where nothing was discarded -->
+            <param name="in_fasta" value="fasta_before_subsample_small.fasta" ftype="fasta"/>
+            <param name="in_fasta_subsampled" value="fasta_after_subsample_small.fasta" ftype="fasta"/>
+            <param name="in_group" value="groups_before_subsample_small.groups" ftype="mothur.groups"/>
+            <param name="in_group_subsampled" value="groups_after_subsample_small.groups" ftype="mothur.groups"/>
+            <param name="threshold" value="1"/>
+            <output name="out_fasta" file="fasta_after_subsample_small.fasta"/>
+            <output name="out_group" file="groups_after_subsample_small.groups"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**