Mercurial > repos > iuc > umi_tools_extract
diff umi-tools_extract.xml @ 8:3cfd8e1073d7 draft
planemo upload commit f6178c9e071a2158a35b82a3607f6dc8a767675c
author | iuc |
---|---|
date | Mon, 16 Jul 2018 17:35:16 -0400 |
parents | f77bc14eba31 |
children | 828dba98cdb4 |
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--- a/umi-tools_extract.xml Sat Jul 14 06:14:14 2018 -0400 +++ b/umi-tools_extract.xml Mon Jul 16 17:35:16 2018 -0400 @@ -1,7 +1,23 @@ -<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> + <macro name="out_conditional"> + <actions> + <conditional name="input_type.type"> + <when value="paired_collection" > + <action type="format"> + <option type="from_param" name="input_type.input_readpair" param_attribute="forward.ext" /> + </action> + </when> + <when value="paired" > + <action type="format"> + <option type="from_param" name="input_type.input_read1" param_attribute="ext" /> + </action> + </when> + </conditional> + </actions> + </macro> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -137,15 +153,18 @@ </conditional> </inputs> <outputs> - <data name="out" format_source="input_single"> + <data name="out" format_source="input_single" label="Reads: ${tool.name} on ${on_string}" > <filter>input_type['type'] == "single"</filter> </data> - <data name="out1" format_source="input_read1"> - <filter>input_type['type'] !== "single"</filter> + <data name="out1" format_source="input_read1" label="Reads1: ${tool.name} on ${on_string}" > + <filter>input_type['type'] != "single"</filter> + <expand macro="out_conditional" /> </data> - <data name="out2" format_source="input_read2"> - <filter>input_type['type'] !== "single"</filter> + <data name="out2" format_source="input_read2" label="Reads2: ${tool.name} on ${on_string}" > + <filter>input_type['type'] != "single"</filter> + <expand macro="out_conditional" /> </data> + <data name="out_log" format="txt"> <filter>print_log == True</filter> </data> @@ -159,30 +178,47 @@ <param name="quality_selector" value="true" /> <param name="quality_filter_threshold" value="10" /> <param name="quality_encoding" value="phred33" /> - <output name="out" file="out_SE.fastq" /> - <output name="out_log" file="out_single.log" lines_diff="22"/> + <output name="out" file="out_SE.fastq" ftype="fastq" /> + <output name="out_log" > + <assert_contents> + <has_text text="Input Reads: 100" /> + <has_text text="umi quality: 28" /> + <has_text text="Reads output: 72" /> + </assert_contents> + </output> </test> <test> <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" /> <param name="bc_pattern" value="NNNXXX" /> - <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" /> - <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" /> - <output name="out_log" file="out_paired.log" lines_diff="16"/> + <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" ftype="fastq.gz" /> + <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" ftype="fastq.gz" /> + <output name="out_log" > + <assert_contents> + <has_text text="Input Reads: 100" /> + <has_text text="Reads output: 100" /> + </assert_contents> + </output> </test> <test> <param name="type" value="paired_collection" /> <!-- same as before, but uncompressed --> + <param name="paired_type" value="no" /> <param name="input_readpair" > - <collection type="paired"> + <collection type="paired" > <element name="forward" ftype="fastq" value="t_R1.fastq" /> <element name="reverse" ftype="fastq" value="t_R2.fastq" /> </collection> </param> <param name="bc_pattern" value="NNNXXX" /> - <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" /> - <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" /> - <output name="out_log" file="out_paired.log" lines_diff="25" /> + <output name="out1" file="out_R1.fastq" ftype="fastq" /> + <output name="out2" file="out_R2.fastq" ftype="fastq" /> + <output name="out_log" > + <assert_contents> + <has_text text="Input Reads: 100" /> + <has_text text="Reads output: 100" /> + </assert_contents> + </output> </test> <test> <param name="type" value="paired" /> @@ -192,7 +228,7 @@ <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" /> <param name="use_barcodes" value="yes" /> <param name="filter_barcode_file" value="scrb_seq_barcodes" /> - <output name="out2" file="scrb_extract.fastq.gz" decompress="true" /> + <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastq.gz" /> </test> <test><!-- same as above but with regex barcode--> <param name="type" value="paired" /> @@ -202,7 +238,16 @@ <param name="bc_pattern" value="^(?P<cell_1>.{6})(?P<umi_1>.{10})" /> <param name="use_barcodes" value="yes" /> <param name="filter_barcode_file" value="scrb_seq_barcodes" /> - <output name="out2" file="scrb_extract.fastq.gz" decompress="true" /> + <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastq.gz" /> + </test> + <test><!-- 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" /> + <param name="extract_method" value="string" /> + <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" /> </test> </tests> <help><![CDATA[