diff fastq_to_fasta.xml @ 5:8979c288aefb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 415a5c5de30530910f3039e5fc66aa15103c6f20

--- a/fastq_to_fasta.xml	Thu Jan 30 13:29:38 2020 -0500
+++ b/fastq_to_fasta.xml	Tue Jun 27 17:37:28 2023 +0000
@@ -9,7 +9,11 @@
 $SKIPN
 $RENAMESEQ
 -v @FQQUAL@
-@GZIP@ > '$output'
+#if $compress_output == 'yes' or ($compress_output == 'infer' and ($input.ext.endswith('.gz') or $input.ext.endswith('.bz2'))):
+    | gzip -c  > '$output_gz'
+#else:
+    > '$output'
+#end if
     ]]></command>
     <inputs>
         <expand macro="fastq_input" />
@@ -21,32 +25,70 @@
             <option value="-r">yes</option>
             <option value="">no</option>
         </param>
+        <param name="compress_output" type="select" label="Compress output FASTA">
+            <option value="infer" selected="true">Infer from input data</option>
+            <option value="yes">Yes</option>
+            <option value="no">No</option>
+        </param>
     </inputs>
     <outputs>
-        <data name="output" format="fasta" metadata_source="input" />
+        <data name="output" format="fasta" metadata_source="input" label="${tool.name} on ${on_string}: FASTA">
+            <filter>
+                compress_output == 'no' or compress_output == 'infer' and not (input.ext.endswith('.gz') or input.ext.endswith('.bz2'))
+            </filter>
+        </data>
+        <data name="output_gz" format="fasta.gz" metadata_source="input" label="${tool.name} on ${on_string}: FASTA.gz">
+            <filter>
+                compress_output == 'yes' or compress_output == 'infer' and input.ext.endswith('.gz') or input.ext.endswith('.bz2')
+            </filter>
+        </data>
     </outputs>
     <tests>
-        <test>
-            <!-- FASTQ-To-FASTA, keep N, don't rename -->
+        <test expect_num_outputs="1" >
+            <!-- 1 FASTQ-To-FASTA, keep N, don't rename -->
             <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
             <param name="SKIPN" value=""/>
             <param name="RENAMESEQ" value=""/>
             <output name="output" file="fastq_to_fasta1a.out" />
         </test>
-        <test>
-            <!-- FASTQ-To-FASTA, discard N, rename -->
+        <test expect_num_outputs="1" >
+            <!-- 2 FASTQ-To-FASTA, discard N, rename -->
             <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
             <param name="SKIPN" value="no"/>
             <param name="RENAMESEQ" value="yes"/>
             <output name="output" file="fastq_to_fasta1b.out" />
         </test>
-        <test>
-            <!-- FASTQ-To-FASTA, discard N, rename -->
+        <test expect_num_outputs="1" >
+            <!-- 3 FASTQ-To-FASTA, discard N, rename -->
             <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" />
             <param name="SKIPN" value="no"/>
             <param name="RENAMESEQ" value="yes"/>
             <output name="output" file="fastq_to_fasta-out2.out" />
         </test>
+        <test expect_num_outputs="1" >
+            <!-- 4 Infer FASTQ.GZ-To-FASTA.GZ -->
+            <param name="input" value="fastq_to_fasta-in2.fastq.gz" ftype="fastqsanger.gz" />
+            <param name="SKIPN" value="no"/>
+            <param name="RENAMESEQ" value="yes"/>
+            <param name="compress_output" value="infer"/>
+            <output name="output" file="fastq_to_fasta-out2.out.gz" compare="sim_size" delta="50" />
+        </test>
+        <test expect_num_outputs="1" >
+            <!-- 5 Force FASTQ.GZ-To-FASTA -->
+            <param name="input" value="fastq_to_fasta-in2.fastq.gz" ftype="fastqsanger.gz" />
+            <param name="SKIPN" value="no"/>
+            <param name="RENAMESEQ" value="yes"/>
+            <param name="compress_output" value="no"/>
+            <output name="output" file="fastq_to_fasta-out2.out"/>
+        </test>
+        <test expect_num_outputs="1" >
+            <!-- 6 Force FASTQ-To-FASTA.GZ -->
+            <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" />
+            <param name="SKIPN" value="no"/>
+            <param name="RENAMESEQ" value="yes"/>
+            <param name="compress_output" value="yes"/>
+            <output name="output" file="fastq_to_fasta-out2.out.gz" compare="sim_size" delta="50" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**