Mercurial > repos > iuc > umi_tools_extract

changeset 14:9fa7803d1c51 draft

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"planemo upload commit 59c614a9dda4b9f49bd3349fbde968ee5eca1db6"
author iuc
date Wed, 02 Jun 2021 18:27:33 +0000
parents 6a675c3aa610
children 27ac32a22ad2
files umi-tools_extract.xml
diffstat 1 files changed, 8 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/umi-tools_extract.xml	Wed Feb 10 19:31:10 2021 +0000
+++ b/umi-tools_extract.xml	Wed Jun 02 18:27:33 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.1">
+<tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.2">
     <description>Extract UMI from fastq files</description>
     <macros>
         <import>macros.xml</import>
@@ -68,8 +68,6 @@
             #end if
             #if $print_log == "1":
                 --log='$out_log'
-            #else
-                --supress-stats
             #end if
         #if $gz:
             #if $input_type.type == 'single':
@@ -153,7 +151,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="type" value="single" />
             <param name="input_single" value="t_R1.fastq" ftype="fastq" />
             <param name="bc_pattern" value="XXXNNN" />
@@ -170,7 +168,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="type" value="paired" />
             <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" />
             <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" />
@@ -184,7 +182,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="type" value="paired_collection" /> <!-- same as before, but uncompressed -->
             <param name="paired_type" value="no" />
             <param name="input_readpair" >
@@ -203,7 +201,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="type" value="paired" />
             <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" />
             <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" />
@@ -213,7 +211,7 @@
             <param name="filter_barcode_file" value="scrb_seq_barcodes" />
             <output name="out2" file="scrb_extract.fastq.gz" decompress="true"  ftype="fastq.gz" />
         </test>
-        <test><!-- same as above but with regex barcode-->
+        <test expect_num_outputs="3"><!-- same as above but with regex barcode-->
             <param name="type" value="paired" />
             <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" />
             <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" />
@@ -223,7 +221,7 @@
             <param name="filter_barcode_file" value="scrb_seq_barcodes" />
             <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastq.gz" />
         </test>
-        <test><!-- CelSeq2 example -->
+        <test expect_num_outputs="2"><!-- CelSeq2 example -->
             <param name="type" value="paired" />
             <param name="input_read1" value="read_R1.200.gz" ftype="fastq.gz" />
             <param name="input_read2" value="read_R2.200.gz" ftype="fastq.gz" />
@@ -231,6 +229,7 @@
             <param name="bc_pattern" value="NNNNNNCCCCCC" />
             <output name="out1" file="read_R1.200_extracted.fastq.gz" ftype="fastq.gz" decompress="true" lines_diff="1" />
             <output name="out2" file="read_R2.200_extracted.fastq.gz" ftype="fastq.gz" decompress="true" lines_diff="1" />
+            <param name="print_log" value="false"/>
         </test>
     </tests>
     <help><![CDATA[