Mercurial > repos > iuc > krakentools_extract_kraken_reads

diff extract_kraken_reads.xml @ 1:f329328da134 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit f37828f1d6b9c53cc2e7ea334ee9a2fb8dbd8711
author iuc
date Tue, 20 Jun 2023 20:03:09 +0000
parents 519e0835abd7
children
line wrap: on
line diff
--- a/extract_kraken_reads.xml	Wed Mar 15 18:18:27 2023 +0000
+++ b/extract_kraken_reads.xml	Tue Jun 20 20:03:09 2023 +0000
@@ -15,11 +15,37 @@
         #if $library.type == 'paired':
             #set input_1 = $library.input_1
             #set input_2 = $library.input_2
+
+            ## tool needs a file ending with gz to work
+            #if $library.input_1.datatype.file_ext.endswith("gz"):
+                ln -s '$input_1' input_1.gz &&
+                ln -s '$input_2' input_2.gz &&
+                #set input_1 = 'input_1.gz'
+                #set input_2 = 'input_2.gz'
+            #end if 
+
         #else if $library.type == 'paired_collection'
             #set input_1 = $library.input_1.forward
             #set input_2 = $library.input_1.reverse
+
+            ## tool needs a file ending with gz to work
+            #if $library.input_1.forward.datatype.file_ext.endswith("gz"):
+                ln -s '$input_1' input_1.gz &&
+                ln -s '$input_2' input_2.gz &&
+                #set input_1 = 'input_1.gz'
+                #set input_2 = 'input_2.gz'
+            #end if 
+
+
         #else
             #set input_1 = $library.input_1
+
+            ## tool needs a file ending with gz to work
+            #if $library.input_1.datatype.file_ext.endswith("gz"):
+                ln -s '$input_1' input_1.gz && 
+                #set input_1 = 'input_1.gz'
+            #end if 
+
         #end if
 
         ## name output according to --fastq_output param
@@ -31,7 +57,6 @@
             #set temp_output_1 = 'output_1.fastq'
             #set temp_output_2 = 'output_2.fastq'
         #end if
-
         ## do not quote $taxid
         extract_kraken_reads.py
         -k '$results'
@@ -76,14 +101,14 @@
                 </option>
             </param>
             <when value="single">
-                <param name="input_1" format="fastq,fasta" type="data" label="FASTQ/A file" help="FASTQ or FASTQ input reads (may be gzipped)" />
+                <param name="input_1" format="fastq,fasta,fastq.gz,fasta.gz" type="data" label="FASTQ/A file" help="FASTQ or FASTQ input reads (may be gzipped)" />
             </when>
             <when value="paired">
-                <param name="input_1" format="fastq,fasta" type="data" label="FASTQ/A forward file" help="FASTQ or FASTQ input reads (may be gzipped)" />
-                <param name="input_2" format="fastq,fasta" type="data" label="FASTQ/A reverse file" help="FASTQ or FASTQ input reads (for paired reads, may be gzipped)" />
+                <param name="input_1" format="fastq,fasta,fastq.gz,fasta.gz" type="data" label="FASTQ/A forward file" help="FASTQ or FASTQ input reads (may be gzipped)" />
+                <param name="input_2" format="fastq,fasta,fastq.gz,fasta.gz" type="data" label="FASTQ/A reverse file" help="FASTQ or FASTQ input reads (for paired reads, may be gzipped)" />
             </when>
             <when value="paired_collection">
-                <param name="input_1" format="fastq,fasta" type="data_collection" collection_type="paired" label="Paired Collection" help="FASTQ or FASTA read pair collection (may be gzipped)" />
+                <param name="input_1" format="fastq,fasta,fastq.gz,fasta.gz" type="data_collection" collection_type="paired" label="Paired Collection" help="FASTQ or FASTA read pair collection (may be gzipped)" />
             </when>
         </conditional>
         <param name="results" argument="-k" format="tabular" type="data" label="Results" help="Results (classification) file from Kraken/KrakenUniq/Kraken2" />
@@ -129,9 +154,17 @@
         </collection>
     </outputs>
     <tests>
-        <!-- test Kraken2 input, single input -->
+        <!-- test Kraken2 input, single input, unzipped -->
         <test expect_num_outputs="1">
-            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />
+            <param name="input_1" value="extract_kraken_reads/R1.fq" ftype="fastq" />
+            <param name="library|type" value="single" />
+            <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" />
+            <param name="taxid" value="11176" />
+            <output name="output_1" file="extract_kraken_reads/out1.k2.11176.fa" decompress="true" ftype="fasta.gz"  />
+        </test>        
+        <!-- test Kraken2 input, single input, zipped -->
+        <test expect_num_outputs="1">
+            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastq.gz" />
             <param name="library|type" value="single" />
             <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" />
             <param name="taxid" value="11176" />
@@ -139,8 +172,8 @@
         </test>
         <!-- test paired input -->
         <test expect_num_outputs="2">
-            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />
-            <param name="input_2" value="extract_kraken_reads/R2.fq.gz" ftype="fastqsanger" />
+            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastq.gz" />
+            <param name="input_2" value="extract_kraken_reads/R2.fq.gz" ftype="fastq.gz" />
             <param name="library|type" value="paired" />
             <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" />
             <param name="taxid" value="11176" />
@@ -151,8 +184,8 @@
         <test expect_num_outputs="3">
             <param name="input_1">
                 <collection type="paired">
-                    <element name="forward" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />
-                    <element name="reverse" value="extract_kraken_reads/R2.fq.gz" ftype="fastqsanger" />
+                    <element name="forward" value="extract_kraken_reads/R1.fq.gz" ftype="fastq.gz" />
+                    <element name="reverse" value="extract_kraken_reads/R2.fq.gz" ftype="fastq.gz" />
                 </collection>
             </param>
             <param name="library|type" value="paired_collection" />
@@ -165,7 +198,7 @@
         </test>
         <!-- test Kraken1 input, include children -->
         <test expect_num_outputs="1">
-            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />
+            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastq.gz" />
             <param name="library|type" value="single" />
             <param name="results" value="extract_kraken_reads/kraken1.results" ftype="tabular" />
             <param name="report" value="extract_kraken_reads/kraken1.report" ftype="tabular" />
@@ -175,7 +208,7 @@
         </test>
         <!-- test exclude -->
         <test expect_num_outputs="1">
-            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />
+            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastq.gz" />
             <param name="library|type" value="single" />
             <param name="results" value="extract_kraken_reads/kraken1.results" ftype="tabular" />
             <param name="report" value="extract_kraken_reads/kraken1.report" ftype="tabular" />
@@ -186,7 +219,7 @@
         </test>
         <!-- test max -->
         <test expect_num_outputs="1">
-            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />
+            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastq.gz" />
             <param name="library|type" value="single" />
             <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" />
             <param name="taxid" value="11176" />
@@ -195,7 +228,7 @@
         </test>
         <!-- test include parents -->
         <test expect_num_outputs="1">
-            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />
+            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastq.gz" />
             <param name="library|type" value="single" />
             <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" />
             <param name="taxid" value="11176" />
@@ -205,7 +238,7 @@
         </test>
         <!-- test multiple tax IDs -->
         <test expect_num_outputs="1">
-            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />
+            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastq.gz" />
             <param name="library|type" value="single" />
             <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" />
             <param name="taxid" value="10386 11176" />
@@ -216,14 +249,14 @@
         </test>
         <!-- test multiple tax IDs -->
         <test expect_failure="true">
-            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />
+            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastq.gz" />
             <param name="library|type" value="single" />
             <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" />
             <param name="taxid" value="10386 f5" />
         </test>
         <!-- test FASTQ output -->
         <test expect_num_outputs="1">
-            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastqsanger" />
+            <param name="input_1" value="extract_kraken_reads/R1.fq.gz" ftype="fastq.gz" />
             <param name="library|type" value="single" />
             <param name="results" value="extract_kraken_reads/kraken2.results" ftype="tabular" />
             <param name="taxid" value="11176" />
@@ -248,4 +281,4 @@
         <person givenName="Jeremy" familyName="Volkening" url="https://github.com/jvolkening" />
         <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" />
     </creator>
-</tool>
+</tool>
\ No newline at end of file