removing uploaded wrong files

tools/chewbbaca/AlleleCall.xml

@@ -5,12 +5,12 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir ./input &&
-        mkdir ./schema &&
+        mkdir './input' &&
+        mkdir './schema' &&
         #for $file in $input_file
-        cp $file ./input/${file.element_identifier} &&
+        cp $file './input/${file.element_identifier}' &&
         #end for
-        unzip $input_schema -d ./schema &&
+        unzip $input_schema -d './schema' &&
         chewBBACA.py AlleleCall
             #if str($training_file) != 'None'
                 --ptf $training_file
@@ -23,7 +23,7 @@
             --pm $prodigal_mode
             --mode $mode
             --force-continue
-            -i ./input -g ./schema/schema_seed/ -o ./output
+            -i './input' -g './schema/schema_seed/' -o './output'
     ]]></command>
     <inputs>
         <param format="fasta" name="input_file" type="data" multiple="true" label="Genome assemblies in FASTA format"/>

tools/chewbbaca/CreateSchema.xml

@@ -5,9 +5,9 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir ./input &&
+        mkdir './input' &&
         #for $file in $input_file
-        cp $file ./input/${file.element_identifier} &&
+        ln -sf $file './input/${file.element_identifier}' &&
         #end for
         chewBBACA.py CreateSchema 
             #if str($training_file) != 'None'
@@ -18,9 +18,9 @@
             --t $translation_table
             --st $size_threshold
             --pm $prodigal_mode
-            -i ./input -o ./output &&
+            -i './input' -o './output' &&
         cd output/ &&
-        zip -r schema_seed.zip ./schema_seed
+        zip -r schema_seed.zip './schema_seed'
     ]]></command>
     <inputs>
         <param format="fasta" name="input_file" type="data" multiple="True" label="Genome assemblies in FASTA format"/>

tools/chewbbaca/PrepExternalSchema.xml

@@ -5,8 +5,8 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir ./schema &&
-        unzip $input_schema -d ./schema &&
+        mkdir './schema' &&
+        unzip '$input_schema' -d './schema' &&
         chewBBACA.py PrepExternalSchema
             #if str($training_file) != 'None'
                 --ptf '$training_file'
@@ -16,8 +16,8 @@
             --t $translation_table
             --st $size_threshold
             $size_filter
-            -g ./schema/schema_seed/ -o ./schema_seed &&
-        zip -r PExternalschema_seed.zip ./schema_seed
+            -g './schema/schema_seed/' -o './schema_seed' &&
+        zip -r PExternalschema_seed.zip './schema_seed'
     ]]></command>
     <inputs>
         <param format="zip" name="input_schema" type="data" multiple="true" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/>

tools/chewbbaca/macros.xml

@@ -12,15 +12,7 @@
     </xml>
     <xml name="citations">
         <citations>
-            <citation type="bibtex">
-            @misc{githubchewBBACA,
-            author = {LastTODO, FirstTODO},
-            year = {TODO},
-            title = {chewBBACA},
-            publisher = {GitHub},
-            journal = {GitHub repository},
-            url = {https://github.com/B-UMMI/chewBBACA}
-            </citation>
+            <citation type="doi">10.1099/mgen.0.000166</citation>
         </citations>
     </xml>
 </macros>