| Previous changeset 13:6a675c3aa610 (2021-02-10) Next changeset 15:27ac32a22ad2 (2021-09-13) |
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Commit message:
"planemo upload commit 59c614a9dda4b9f49bd3349fbde968ee5eca1db6" |
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modified:
umi-tools_extract.xml |
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| diff -r 6a675c3aa610 -r 9fa7803d1c51 umi-tools_extract.xml --- 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[ |