Mercurial > repos > iuc > fastp
diff fastp.xml @ 11:c59d48774d03 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
author | iuc |
---|---|
date | Tue, 05 Mar 2024 08:41:43 +0000 |
parents | dbf9c561ef29 |
children | d60c3f704da0 |
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--- a/fastp.xml Thu Feb 03 17:20:32 2022 +0000 +++ b/fastp.xml Tue Mar 05 08:41:43 2024 +0000 @@ -1,10 +1,11 @@ -<tool id="fastp" name="fastp" version="@WRAPPER_VERSION@+galaxy0"> - <description>- fast all-in-one preprocessing for FASTQ files</description> +<tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy0" profile="23.1"> + <description>fast all-in-one preprocessing for FASTQ files</description> <macros> <import>macros.xml</import> </macros> + <expand macro="biotools" /> <requirements> - <requirement type="package" version="@WRAPPER_VERSION@">fastp</requirement> + <requirement type="package" version="@TOOL_VERSION@">fastp</requirement> </requirements> <version_command>fastp -v</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -24,19 +25,19 @@ #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_%s" % ($single_paired.paired_input.name, "R2"))) + $ext #set out1 = $output_paired_coll.forward #set out2 = $output_paired_coll.reverse - ln -s '$in1' '$in1_name' && - ln -s '$in2' '$in2_name' && + ln -sf '$in1' '$in1_name' && + ln -sf '$in2' '$in2_name' && #else #if $in1.is_of_type('fastq.gz') #set ext = '.fastq.gz' #end if #set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext - ln -s '$in1' '$in1_name' && + ln -sf '$in1' '$in1_name' && #if str($single_paired.single_paired_selector) == 'paired': #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_R2" % $in2.element_identifier)) + $ext - ln -s '$in2' '$in2_name' && + ln -sf '$in2' '$in2_name' && #end if #end if @@ -209,7 +210,6 @@ #end if ]]></command> <inputs> - <conditional name="single_paired"> <param name="single_paired_selector" type="select" label="Single-end or paired reads"> <option value="single" selected="true">Single-end</option> @@ -229,8 +229,8 @@ </expand> <expand macro="global_trimming_options_paired" /> </when> - <when value="paired_collection"> - <param name="paired_input" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Select paired collection(s)"/> + <when value="paired_collection"> + <param name="paired_input" type="data_collection" format="fastq,fastq.gz" label="Select paired collection(s)" collection_type="paired"/> <expand macro="adapter_trimming_options"> <expand macro="adapter_sequence" read_number="2"/> </expand> @@ -255,7 +255,7 @@ <section name="length_filtering_options" title="Length filtering options" expanded="True"> <param name="disable_length_filtering" argument="-L" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Disable length filtering" help="Length filtering is enabled by default. If this option is specified, length filtering is disabled."/> <param name="length_required" argument="-l" type="integer" optional="true" label="Length required" help="Reads shorter than this value will be discarded. Default is 15."/> - <param name="length_limit" argument="--length_limit" type="integer" optional="true" label="Maximum length" help="Reads longer than this value will be discarded. Default is 0 and means no limitation."/> + <param argument="--length_limit" type="integer" optional="true" label="Maximum length" help="Reads longer than this value will be discarded. Default is 0 and means no limitation."/> </section> <section name="low_complexity_filter" title="Low complexity filtering options" expanded="True"> @@ -287,17 +287,17 @@ <option value="-x">Enable polyX tail trimming</option> </param> <when value="-x"> - <param name="poly_x_min_len" argument="--poly_x_min_len" type="integer" optional="true" label="PolyX minimum length" - help="The minimum length to detect polyX in the read tail. 10 by default."/> + <param argument="--poly_x_min_len" type="integer" optional="true" label="PolyX minimum length" + help="The minimum length to detect polyX in the read tail. 10 by default."/> </when> <when value="" /> </conditional> <section name="umi_processing" title="UMI processing" expanded="True"> <param name="umi" argument="-U" type="boolean" truevalue="-U" falsevalue="" checked="false" label="Enable unique molecular identifer" help="Enable unique molecular identifer (UMI) preprocessing."/> - <param name="umi_loc" argument="--umi_loc" type="text" optional="true" label="UMI location" help="Specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none."/> - <param name="umi_len" argument="--umi_len" type="integer" optional="true" label="UMI length" help="If the UMI is in read1/read2, its length should be provided."/> - <param name="umi_prefix" argument="--umi_prefix" type="text" optional="true" label="UMI prefix" help="If specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default."/> + <param argument="--umi_loc" type="text" optional="true" label="UMI location" help="Specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none."/> + <param argument="--umi_len" type="integer" optional="true" label="UMI length" help="If the UMI is in read1/read2, its length should be provided."/> + <param argument="--umi_prefix" type="text" optional="true" label="UMI prefix" help="If specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default."/> </section> <section name="cutting_by_quality_options" title="Per read cutting by quality options" expanded="True"> @@ -337,7 +337,7 @@ </outputs> <tests> - <!-- Ensure default output works --> + <!-- 1. Ensure default output works --> <test expect_num_outputs="2"> <param name="in1" ftype="fastqsanger" value="R1.fq"/> <param name="single_paired_selector" value="single"/> @@ -348,7 +348,7 @@ </assert_contents> </output> </test> - <!-- Ensure paired collection works --> + <!-- 2. Ensure paired collection works --> <test expect_num_outputs="4"> <param name="single_paired_selector" value="paired_collection"/> <param name="paired_input"> @@ -367,14 +367,14 @@ <element name="reverse" value="out_bwa2.fq" ftype="fastqsanger"/> </output_collection> </test> - <!-- Ensure custom adapter works --> + <!-- 3. Ensure custom adapter works --> <test expect_num_outputs="2"> <param name="in1" ftype="fastq" value="R1.fq"/> <param name="single_paired_selector" value="single"/> <param name="adapter_sequence1" value="ATCG"/> <output name="out1" ftype="fastq" file="out_a.fq"/> </test> - <!-- Ensure UMI processing works --> + <!-- 4. Ensure UMI processing works --> <test expect_num_outputs="2"> <param name="in1" ftype="fastq" value="R1.fq"/> <param name="single_paired_selector" value="single"/> @@ -385,7 +385,7 @@ </section> <output name="out1" ftype="fastq" file="out2.fq"/> </test> - <!-- Ensure UMI processing with different lengths works --> + <!-- 5. Ensure UMI processing with different lengths works --> <test expect_num_outputs="2"> <param name="in1" ftype="fastq" value="R1.fq"/> <param name="single_paired_selector" value="single"/> @@ -396,7 +396,7 @@ </section> <output name="out1" ftype="fastq" file="out3.fq"/> </test> - <!-- Ensure paired-end fastq works --> + <!-- 6. Ensure paired-end fastq works --> <test expect_num_outputs="3"> <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/> <param name="in2" ftype="fastq" value="bwa-mem-fastq2.fq"/> @@ -404,7 +404,7 @@ <output name="out1" ftype="fastq" file="out_bwa1.fq"/> <output name="out2" ftype="fastq" file="out_bwa2.fq"/> </test> - <!-- Ensure paired-end UMI processing of Read 1 works --> + <!-- 7. Ensure paired-end UMI processing of Read 1 works --> <test expect_num_outputs="3"> <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/> <param name="in2" ftype="fastq" value="bwa-mem-fastq2.fq"/> @@ -417,7 +417,7 @@ <output name="out1" ftype="fastq" file="out_bwa_umi_read1_1.fq"/> <output name="out2" ftype="fastq" file="out_bwa_umi_read1_2.fq"/> </test> - <!-- Ensure paired-end UMI processing of Read 2 works --> + <!-- 8. Ensure paired-end UMI processing of Read 2 works --> <test expect_num_outputs="3"> <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/> <param name="in2" ftype="fastq" value="bwa-mem-fastq2.fq"/> @@ -430,7 +430,7 @@ <output name="out1" ftype="fastq" file="out_bwa_umi_read2_1.fq"/> <output name="out2" ftype="fastq" file="out_bwa_umi_read2_2.fq"/> </test> - <!-- Ensure JSON report output works --> + <!-- 9. Ensure JSON report output works --> <test expect_num_outputs="2"> <param name="in1" ftype="fastqsanger" value="R1.fq"/> <param name="single_paired_selector" value="single"/> @@ -443,7 +443,7 @@ </assert_contents> </output> </test> - <!-- Ensure polyG trimming works --> + <!-- 10. Ensure polyG trimming works --> <test expect_num_outputs="2"> <param name="in1" ftype="fastq.gz" value="R1.fq.gz"/> <param name="single_paired_selector" value="single"/> @@ -451,7 +451,7 @@ <param name="poly_g_min_len" value="10"/> <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/> </test> - <!-- Ensure polyX trimming works --> + <!-- 11. Ensure polyX trimming works --> <test expect_num_outputs="2"> <param name="in1" ftype="fastq.gz" value="R1.fq.gz"/> <param name="single_paired_selector" value="single"/> @@ -460,13 +460,24 @@ <param name="poly_x_min_len" value="10"/> <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/> </test> + <!-- 12. Test fastq files with different length --> + <test expect_exit_code="255" expect_failure="true"> + <param name="single_paired_selector" value="paired_collection"/> + <param name="paired_input"> + <collection type="paired"> + <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> + <element name="reverse" value="bwa-mem-fastq2_too_long.fq" ftype="fastqsanger" /> + </collection> + </param> + </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** -fastp_ is a tool designed to provide fast all-in-one preprocessing for FASTQ files. This tool is developed in C++ with multithreading supported to afford high performance. +fastp_ is a tool designed to provide fast all-in-one preprocessing for FASTQ files. This tool is developed in C++ with multithreading supported to +afford high performance. *Features*