Mercurial > repos > iuc > stacks2_procrad
diff stacks_procrad.xml @ 2:bd5ff77e2036 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
| author | iuc |
|---|---|
| date | Wed, 15 Jul 2020 17:33:16 -0400 |
| parents | ca7aa77c7f57 |
| children | b4bab607eb05 |
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--- a/stacks_procrad.xml Mon Sep 30 14:20:50 2019 -0400 +++ b/stacks_procrad.xml Wed Jul 15 17:33:16 2020 -0400 @@ -8,6 +8,9 @@ <expand macro="version_cmd"/> <command detect_errors="aggressive"><![CDATA[ @FASTQ_INPUT_FUNCTIONS@ + +python '$__tool_directory__'/check_bcfile.py '$barcode' && + mkdir stacks_inputs stacks_outputs && #if $output_log @@ -69,8 +72,8 @@ <section name="options_advanced" title="advanced options" expanded="False"> <expand macro="common_advanced"/> - <param argument="--bestrad" type="boolean" checked="false" truevalue="--bestrad" falsevalue="" label="Library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads" /> - <param argument="--disable_rad_check" type="boolean" checked="false" truevalue="--disable_rad_check" falsevalue="" label="Disable checking if the RAD site is intact" /> + <param argument="--bestrad" type="boolean" checked="false" truevalue="--bestrad" falsevalue="" label="Library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads"/> + <param argument="--disable_rad_check" type="boolean" checked="false" truevalue="--disable_rad_check" falsevalue="" label="Disable checking if the RAD site is intact"/> <expand macro="rescue_barcode"/> <expand macro="process_adapter"/> </section> @@ -86,22 +89,22 @@ </outputs> <tests> <!-- single single ended input, no filtering (hence no capturing) + log --> - <test> + <test expect_num_outputs="2"> <param name="input_type|input_type_select" value="single"/> <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/> <param name="input_type|barcode_encoding" value="--inline_null"/> <param name="barcode" value="procrad/barcodes"/> <param name="options_enzyme|options_enzyme_selector" value="1"/> <param name="options_enzyme|enzyme" value="ecoRI"/> - <param name="add_log" value="yes" /> + <param name="add_log" value="yes"/> <output name="output_log" file="procrad/process_radtags.out" lines_diff="4"/> <output_collection name="demultiplexed" count="40"> - <element name="PopA_01" file="demultiplexed/PopA_01.fq" ftype="fastqsanger" /> + <element name="PopA_01" file="demultiplexed/PopA_01.fq" ftype="fastqsanger"/> </output_collection> </test> <!-- multiple (zipped) single end input (misusing R2 as add single end read file), discarding by quality and capturing them --> - <test> + <test expect_num_outputs="3"> <param name="input_type|input_type_select" value="single"/> <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip,procrad/R2.fq.gzip"/> <param name="input_type|barcode_encoding" value="--inline_null"/> @@ -110,19 +113,19 @@ <param name="options_enzyme|enzyme" value="ecoRI"/> <param name="filter_cond|filter_select" value="yes"/> <param name="filter_cond|discard" value="-q"/> - <param name="filter_cond|sliding" value="0.1" /> - <param name="filter_cond|score" value="11" /> - <param name="filter_cond|remove" value="-c" /> + <param name="filter_cond|sliding" value="0.1"/> + <param name="filter_cond|score" value="11"/> + <param name="filter_cond|remove" value="-c"/> <param name="capture" value="-D"/> <param name="outype" value="gzfastq"/> - <param name="add_log" value="yes" /> + <param name="add_log" value="yes"/> <output name="output_log" file="procrad/process_radtags2.out" lines_diff="4"/> <assert_command> - <has_text text="-q" /> - <has_text text="-w 0.1" /> - <has_text text="-s 11" /> - <has_text text="-c" /> - <has_text text="-D" /> + <has_text text="-q"/> + <has_text text="-w 0.1"/> + <has_text text="-s 11"/> + <has_text text="-c"/> + <has_text text="-D"/> </assert_command> <output_collection name="demultiplexed" count="40"> <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/> @@ -133,13 +136,13 @@ </output_collection> </test> <!-- paired input, no quality but length filter, gzfasta output --> - <test> + <test expect_num_outputs="4"> <param name="input_type|input_type_select" value="paired"/> <param name="input_type|fqinputs"> <collection type="list:paired"> <element name="reads"> <collection type="paired"> - <element name="forward" value="procrad/R1.fq" ftype="fastqsanger" /> + <element name="forward" value="procrad/R1.fq" ftype="fastqsanger"/> <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/> </collection> </element> @@ -152,15 +155,15 @@ <param name="filter_cond|len_limit" value="50"/> <param name="capture" value="-D"/> <param name="outype" value="gzfasta"/> - <param name="add_log" value="yes" /> + <param name="add_log" value="yes"/> <output name="output_log" file="procrad/process_radtags_paired.out" lines_diff="4"/> <assert_command> - <has_text text="--len_limit 50" /> + <has_text text="--len_limit 50"/> </assert_command> <output_collection name="demultiplexed_paired" type="list:paired" count="40"> <element name="PopA_01"> - <element name="forward" value="demultiplexed/PopA_01.1.fa.gz" ftype="fasta.gz" /> - <element name="reverse" value="demultiplexed/PopA_01.2.fa.gz" ftype="fasta.gz" /> + <element name="forward" value="demultiplexed/PopA_01.1.fa.gz" ftype="fasta.gz"/> + <element name="reverse" value="demultiplexed/PopA_01.2.fa.gz" ftype="fasta.gz"/> </element> </output_collection> <output_collection name="remaining" type="list:paired" count="40"> @@ -177,13 +180,13 @@ </output_collection> </test> <!-- paired input (gzipped) + advanced options + two enzymes, fasta output --> - <test> + <test expect_num_outputs="3"> <param name="input_type|input_type_select" value="paired"/> <param name="input_type|fqinputs"> <collection type="list:paired"> <element name="reads"> <collection type="paired"> - <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz" /> + <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz"/> <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/> </collection> </element> @@ -193,30 +196,30 @@ <param name="options_enzyme|options_enzyme_selector" value="2"/> <param name="options_enzyme|enzyme" value="ecoRI"/> <param name="options_enzyme|enzyme2" value="ecoRI"/> - <param name="options_advanced|truncate" value="70" /> + <param name="options_advanced|truncate" value="70"/> <param name="options_advanced|rescue_cond|rescue" value="-r"/> - <param name="options_advanced|rescue_cond|barcode_dist_1" value="2" /> - <param name="options_advanced|rescue_cond|barcode_dist_2" value="2" /> - <param name="options_advanced|bestrad" value="--bestrad" /> + <param name="options_advanced|rescue_cond|barcode_dist_1" value="2"/> + <param name="options_advanced|rescue_cond|barcode_dist_2" value="2"/> + <param name="options_advanced|bestrad" value="--bestrad"/> <param name="options_advanced|retain_header" value="--retain_header"/> - <param name="options_advanced|disable_rad_check" value="--disable_rad_check" /> - <param name="options_advanced|adapter_1" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" /> - <param name="options_advanced|adapter_2" value="TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" /> - <param name="options_advanced|adapter_mm" value="2" /> + <param name="options_advanced|disable_rad_check" value="--disable_rad_check"/> + <param name="options_advanced|adapter_1" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"/> + <param name="options_advanced|adapter_2" value="TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"/> + <param name="options_advanced|adapter_mm" value="2"/> <param name="outype" value="fasta"/> <assert_command> - <has_text text="-e ecoRI" /> - <has_text text="--renz_2 ecoRI" /> - <has_text text="-t 70" /> - <has_text text="-r" /> - <has_text text="--bestrad" /> - <has_text text="--retain_header" /> - <has_text text="--disable_rad_check" /> - <has_text text="--barcode_dist_1 2" /> - <has_text text="--barcode_dist_2 2" /> - <has_text text="--adapter_1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" /> - <has_text text="--adapter_2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" /> - <has_text text="--adapter_mm 2" /> + <has_text text="-e ecoRI"/> + <has_text text="--renz_2 ecoRI"/> + <has_text text="-t 70"/> + <has_text text="-r"/> + <has_text text="--bestrad"/> + <has_text text="--retain_header"/> + <has_text text="--disable_rad_check"/> + <has_text text="--barcode_dist_1 2"/> + <has_text text="--barcode_dist_2 2"/> + <has_text text="--adapter_1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"/> + <has_text text="--adapter_2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"/> + <has_text text="--adapter_mm 2"/> </assert_command> <output_collection name="demultiplexed_paired" type="list:paired" count="40"> <element name="PopA_01"> @@ -226,13 +229,42 @@ </output_collection> <output_collection name="remaining" type="list:paired" count="40"> <element name="PopA_01"> - <element name="forward" file="demultiplexed/PopA_01.rem.1.fa" ftype="fasta" /> - <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa" ftype="fasta" /> + <element name="forward" file="demultiplexed/PopA_01.rem.1.fa" ftype="fasta"/> + <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa" ftype="fasta"/> </element> </output_collection> </test> + <!-- test invalid barcode file --> + <test expect_failure="true"> + <param name="input_type|input_type_select" value="single"/> + <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/> + <param name="input_type|barcode_encoding" value="--inline_null"/> + <param name="barcode" value="procrad/barcodes-duplicate"/> + <param name="options_enzyme|options_enzyme_selector" value="1"/> + <param name="options_enzyme|enzyme" value="ecoRI"/> + <param name="add_log" value="yes"/> + </test> + <!-- test invalid barcode file --> + <test expect_failure="true"> + <param name="input_type|input_type_select" value="single"/> + <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/> + <param name="input_type|barcode_encoding" value="--inline_null"/> + <param name="barcode" value="procrad/barcodes-duplicate2"/> + <param name="options_enzyme|options_enzyme_selector" value="1"/> + <param name="options_enzyme|enzyme" value="ecoRI"/> + <param name="add_log" value="yes"/> + </test> + <!-- test invalid barcode file --> + <test expect_failure="true"> + <param name="input_type|input_type_select" value="single"/> + <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/> + <param name="input_type|barcode_encoding" value="--inline_null"/> + <param name="barcode" value="procrad/barcodes-duplicate3"/> + <param name="options_enzyme|options_enzyme_selector" value="1"/> + <param name="options_enzyme|enzyme" value="ecoRI"/> + <param name="add_log" value="yes"/> + </test> </tests> - <help> <![CDATA[ .. class:: infomark @@ -290,5 +322,5 @@ @STACKS_INFOS@ ]]> </help> - <expand macro="citation" /> + <expand macro="citation"/> </tool>