Mercurial > repos > iuc > read_it_and_keep
diff read-it-and-keep.xml @ 1:1563b58905f4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
| author | iuc |
|---|---|
| date | Thu, 17 Mar 2022 11:12:09 +0000 |
| parents | 554aa2a63f04 |
| children | fa7086274673 |
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--- a/read-it-and-keep.xml Fri Jan 28 18:47:34 2022 +0000 +++ b/read-it-and-keep.xml Thu Mar 17 11:12:09 2022 +0000 @@ -1,12 +1,13 @@ <tool id="read_it_and_keep" name="Read It and Keep" version="@TOOL_VERSION@+galaxy0" profile="20.09"> <macros> - <token name="@FASTQ_FORMATS@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token> - <token name="@TOOL_VERSION@">0.1.0</token> + <token name="@INPUT_FORMATS@">fasta,fastq,fasta.gz,fastq.gz</token> + <token name="@TOOL_VERSION@">0.2.2</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">read-it-and-keep</requirement> - <requirement type="package">python</requirement> + <requirement type="package" version="3.10">python</requirement> </requirements> + <version_command><![CDATA[readItAndKeep -V]]></version_command> <command detect_errors="exit_code"><![CDATA[ #if $ref_source.source == "history" ln -s '$ref_source.ref_fasta' ref${trim_reference}.fasta && @@ -17,26 +18,43 @@ python '$__tool_directory__/trim_reference.py' ref${trim_reference}.fasta ref.fasta && #end if #if $reads.read_type == "paired" - ln -s '$reads.read1' read1.fastq && - ln -s '$reads.read2' read2.fastq && + #set $ext_out1 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq' + #set $ext_out2 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq' + ln -s '$reads.read1' read1 && + ln -s '$reads.read2' read2 && #elif $reads.read_type == 'paired_collection' - ln -s '$reads.paired_reads.forward' read1.fastq && - ln -s '$reads.paired_reads.reverse' read2.fastq && + #set $ext_out1 = 'fasta' if $reads.paired_reads.forward.ext in ['fasta', 'fasta.gz'] else 'fastq' + #set $ext_out2 = 'fasta' if $reads.paired_reads.reverse.ext in ['fasta', 'fasta.gz'] else 'fastq' + ln -s '$reads.paired_reads.forward' read1 && + ln -s '$reads.paired_reads.reverse' read2 && #elif $reads.read_type == 'single' - ln -s '$reads.single_read1' read1.fastq && + #set $ext_out1 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq' + ln -s '$reads.read1' read1 && #end if readItAndKeep --tech $sequencing_tech --ref_fasta ref.fasta --min_map_length $adv.min_map_length --min_map_length_pc $adv.min_map_length_pc - --reads1 read1.fastq + $adv.enumerate_names + --reads1 read1 #if $reads.read_type != "single" - --reads2 read2.fastq + --reads2 read2 #end if -o output - #if $reads.read_type == 'single' - && mv output.reads.fastq.gz output.reads_1.fastq.gz + #if $reads.read_type == 'single': + && mv output.reads.${ext_out1}.gz output.reads_1.${ext_out1}.gz + #end if + #if $reads.read_type == 'paired_collection': + #if not $reads.paired_reads.forward.ext.endswith('.gz'): + && gunzip ./output.reads_1.${ext_out1}.gz + && gunzip ./output.reads_2.${ext_out2}.gz + #end if + #elif not $reads.read1.ext.endswith('.gz'): + && gunzip ./output.reads_1.${ext_out1}.gz + #if $reads.read_type != 'single' and not $reads.read2.ext.endswith('.gz'): + && gunzip ./output.reads_2.${ext_out2}.gz + #end if #end if ]]></command> <inputs> @@ -47,14 +65,14 @@ <option value="single">Single ended</option> </param> <when value="paired"> - <param type="data" format="@FASTQ_FORMATS@" name="read1" label="Read1" /> - <param type="data" format="@FASTQ_FORMATS@" name="read2" label="Read2" /> + <param type="data" format="@INPUT_FORMATS@" name="read1" label="Read1" /> + <param type="data" format="@INPUT_FORMATS@" name="read2" label="Read2" /> </when> <when value="paired_collection"> - <param type="data_collection" collection_type="paired" format="@FASTQ_FORMATS@" name="paired_reads" label="Reads" /> + <param type="data_collection" collection_type="paired" format="@INPUT_FORMATS@" name="paired_reads" label="Reads" /> </when> <when value="single"> - <param type="data" format="@FASTQ_FORMATS@" name="single_read1" label="Read1" /> + <param type="data" format="@INPUT_FORMATS@" name="read1" label="Read1" /> </when> </conditional> <conditional name="ref_source"> @@ -79,22 +97,176 @@ <section name="adv" title="Advanced options"> <param argument="--min_map_length" type="integer" min="0" value="50" label="Shortest match required to keep a read (in bp)" /> <param argument="--min_map_length_pc" type="float" min="0.0" max="100.0" value="50.0" label="Minimum length of match required to keep a read (as percentage of read length" /> + <param name="enumerate_names" type="boolean" truevalue="--enumerate_names" falsevalue="" label="Rename the reads 1,2,3,... (for paired reads, will also add /1 or /2 to the end of names)" /> </section> </inputs> <outputs> - <data name="output_reads1" format="fastqsanger.gz" label="Filtered reads ${on_string} - reads1" from_work_dir="output.reads_1.fastq.gz"> + <data name="output_reads1" format_source="read1" label="Filtered reads ${on_string} - reads1" from_work_dir="output.reads_1.fast*"> <filter>reads["read_type"] == "single" or reads["read_type"] == "paired"</filter> </data> - <data name="output_reads2" format="fastqsanger.gz" label="Filtered reads ${on_string} - reads2" from_work_dir="output.reads_2.fastq.gz"> + <data name="output_reads2" format_source="read2" label="Filtered reads ${on_string} - reads2" from_work_dir="output.reads_2.fast*"> <filter>reads["read_type"] == "paired"</filter> </data> - <collection type="paired" format="fastqsanger.gz" name="output_collection" label="Filtered reads ${on_string}"> + <collection type="paired" name="output_collection" format_source="paired_reads" label="Filtered reads ${on_string}"> <filter>reads["read_type"] == "paired_collection"</filter> - <data name="forward" format="fastqsanger.gz" from_work_dir="output.reads_1.fastq.gz" /> - <data name="reverse" format="fastqsanger.gz" from_work_dir="output.reads_2.fastq.gz" /> + <data name="forward" from_work_dir="output.reads_1.fast*" /> + <data name="reverse" from_work_dir="output.reads_2.fast*" /> </collection> </outputs> <tests> + <!--Testing uncompressed fastq input--> + <test expect_num_outputs="2"> + <conditional name="reads"> + <param name="read_type" value="paired" /> + <param name="read1" value="test1.fastq.gz" ftype="fastqsanger" /> + <param name="read2" value="test2.fastq.gz" ftype="fastqsanger" /> + </conditional> + <conditional name="ref_source"> + <param name="source" value="history" /> + <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> + </conditional> + <param name="sequencing_tech" value="illumina" /> + <output name="output_reads1" file="output.test1.reads_1.fastq" ftype="fastqsanger"/> + <output name="output_reads2" file="output.test1.reads_2.fastq" ftype="fastqsanger"/> + </test> + <test expect_num_outputs="3"> + <conditional name="reads"> + <param name="read_type" value="paired_collection" /> + <param name="paired_reads"> + <collection type="paired"> + <element name="forward" value="test1.fastq.gz" ftype="fastqsanger" /> + <element name="reverse" value="test2.fastq.gz" ftype="fastqsanger" /> + </collection> + </param> + </conditional> + <conditional name="ref_source"> + <param name="source" value="history" /> + <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> + </conditional> + <param name="sequencing_tech" value="illumina" /> + <output_collection name="output_collection" type="paired"> + <element name="forward" file="output.test1.reads_1.fastq" ftype="fastqsanger"/> + <element name="reverse" file="output.test1.reads_2.fastq" ftype="fastqsanger"/> + </output_collection> + </test> + <test expect_num_outputs="1"> + <conditional name="reads"> + <param name="read_type" value="single" /> + <param name="read1" value="test3.fastq.gz" ftype="fastqsanger"/> + </conditional> + <conditional name="ref_source"> + <param name="source" value="history" /> + <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> + </conditional> + <param name="sequencing_tech" value="ont" /> + <param name="enumerate_names" value="True" /> + <output name="output_reads1" file="output.test3.reads_1.fastq" ftype="fastqsanger"/> + </test> + <!--Testing uncompressed fasta input--> + <test expect_num_outputs="2"> + <conditional name="reads"> + <param name="read_type" value="paired" /> + <param name="read1" value="test1.fasta.gz" ftype="fasta" /> + <param name="read2" value="test2.fasta.gz" ftype="fasta" /> + </conditional> + <conditional name="ref_source"> + <param name="source" value="history" /> + <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> + </conditional> + <param name="sequencing_tech" value="illumina" /> + <output name="output_reads1" file="output.test1.reads_1.fasta" ftype="fasta"/> + <output name="output_reads2" file="output.test1.reads_2.fasta" ftype="fasta"/> + </test> + <test expect_num_outputs="3"> + <conditional name="reads"> + <param name="read_type" value="paired_collection" /> + <param name="paired_reads"> + <collection type="paired"> + <element name="forward" value="test1.fasta.gz" ftype="fasta" /> + <element name="reverse" value="test2.fasta.gz" ftype="fasta" /> + </collection> + </param> + </conditional> + <conditional name="ref_source"> + <param name="source" value="history" /> + <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> + </conditional> + <param name="sequencing_tech" value="illumina" /> + <output_collection name="output_collection" type="paired"> + <element name="forward" file="output.test1.reads_1.fasta" ftype="fasta"/> + <element name="reverse" file="output.test1.reads_2.fasta" ftype="fasta"/> + </output_collection> + </test> + <test expect_num_outputs="1"> + <conditional name="reads"> + <param name="read_type" value="single" /> + <param name="read1" value="test3.fasta.gz" ftype="fasta"/> + </conditional> + <conditional name="ref_source"> + <param name="source" value="history" /> + <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> + </conditional> + <param name="sequencing_tech" value="ont" /> + <param name="enumerate_names" value="True" /> + <output name="output_reads1" file="output.test3.reads_1.fasta" ftype="fasta"/> + </test> + <!--Testing compressed fasta input--> + <test expect_num_outputs="2"> + <conditional name="reads"> + <param name="read_type" value="paired" /> + <param name="read1" value="test1.fasta.gz" ftype="fasta.gz" /> + <param name="read2" value="test2.fasta.gz" ftype="fasta.gz" /> + </conditional> + <conditional name="ref_source"> + <param name="source" value="history" /> + <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> + </conditional> + <param name="sequencing_tech" value="illumina" /> + <output name="output_reads1" decompress="true" file="output.test1.reads_1.fasta" ftype="fasta.gz"/> + <output name="output_reads2" decompress="true" file="output.test1.reads_2.fasta" ftype="fasta.gz"/> + </test> + <test expect_num_outputs="3"> + <conditional name="reads"> + <param name="read_type" value="paired_collection" /> + <param name="paired_reads"> + <collection type="paired"> + <element name="forward" value="test1.fasta.gz" ftype="fasta.gz" /> + <element name="reverse" value="test2.fasta.gz" ftype="fasta.gz" /> + </collection> + </param> + </conditional> + <conditional name="ref_source"> + <param name="source" value="history" /> + <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> + </conditional> + <param name="sequencing_tech" value="illumina" /> + <output_collection name="output_collection" type="paired"> + <element name="forward" ftype="fasta.gz"> + <assert_contents> + <has_size value="680" delta="50" /> + </assert_contents> + </element> + <element name="reverse" ftype="fasta.gz"> + <assert_contents> + <has_size value="670" delta="50" /> + </assert_contents> + </element> + </output_collection> + </test> + <test expect_num_outputs="1"> + <conditional name="reads"> + <param name="read_type" value="single" /> + <param name="read1" value="test3.fasta.gz" ftype="fasta.gz"/> + </conditional> + <conditional name="ref_source"> + <param name="source" value="history" /> + <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> + </conditional> + <param name="sequencing_tech" value="ont" /> + <param name="enumerate_names" value="True" /> + <output name="output_reads1" decompress="true" file="output.test3.reads_1.fasta" ftype="fasta.gz"/> + </test> + <!--Testing compressed fastq input--> <test expect_num_outputs="2"> <conditional name="reads"> <param name="read_type" value="paired" /> @@ -106,8 +278,8 @@ <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> </conditional> <param name="sequencing_tech" value="illumina" /> - <output name="output_reads1" value="output_test1.fastq.gz" /> - <output name="output_reads2" value="output_test2.fastq.gz" /> + <output name="output_reads1" decompress="true" file="output.test1.reads_1.fastq" ftype="fastqsanger.gz"/> + <output name="output_reads2" decompress="true" file="output.test1.reads_2.fastq" ftype="fastqsanger.gz"/> </test> <test expect_num_outputs="3"> <conditional name="reads"> @@ -115,7 +287,7 @@ <param name="paired_reads"> <collection type="paired"> <element name="forward" value="test1.fastq.gz" ftype="fastqsanger.gz" /> - <element name="reverse" value="test2.fastq.gz" ftype="fastqsanger.gz" /> + <element name="reverse" value="test2.fastq.gz" ftype="fastqsanger.gz" /> </collection> </param> </conditional> @@ -124,22 +296,31 @@ <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> </conditional> <param name="sequencing_tech" value="illumina" /> - <output_collection name="output_collection"> - <element name="forward" value="output_test1.fastq.gz" /> - <element name="reverse" value="output_test2.fastq.gz" /> + <output_collection name="output_collection" type="paired"> + <element name="forward" ftype="fastqsanger.gz"> + <assert_contents> + <has_size value="995" delta="50" /> + </assert_contents> + </element> + <element name="reverse" ftype="fastqsanger.gz"> + <assert_contents> + <has_size value="960" delta="50" /> + </assert_contents> + </element> </output_collection> </test> <test expect_num_outputs="1"> <conditional name="reads"> <param name="read_type" value="single" /> - <param name="single_read1" value="test3.fastq.gz" ftype="fastqsanger.gz"/> + <param name="read1" value="test3.fastq.gz" ftype="fastqsanger.gz"/> </conditional> <conditional name="ref_source"> <param name="source" value="history" /> <param name="ref_fasta" value="reference.fasta" ftype="fasta" /> </conditional> <param name="sequencing_tech" value="ont" /> - <output name="output_reads1" value="output_test3.fastq.gz" /> + <param name="enumerate_names" value="True" /> + <output name="output_reads1" decompress="true" file="output.test3.reads_1.fastq" ftype="fastqsanger.gz"/> </test> </tests> <help><![CDATA[