Changeset 2:a91455432cd4 (2025-09-12)

Previous changeset 1:d4a96287909e (2020-10-16)

Commit message:
planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981

modified:
cryptogenotyper.xml

added:
test-data/test_illumina_18S_F.fasta
test-data/test_illumina_18S_R.fasta
test-data/test_illumina_gp60_F1.fasta
test-data/test_illumina_gp60_R1.fasta

diff -r d4a96287909e -r a91455432cd4 cryptogenotyper.xml
--- a/cryptogenotyper.xml Fri Oct 16 22:32:56 2020 +0000
+++ b/cryptogenotyper.xml Fri Sep 12 18:50:40 2025 +0000

[

b'@@ -3,7 +3,7 @@\n classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data.\n </description>\n <macros>\n- <token name="@VERSION@">1.0</token>\n+ <token name="@VERSION@">1.5.0</token>\n </macros>\n <requirements>\n <requirement type="package" version ="@VERSION@">cryptogenotyper</requirement>\n@@ -15,20 +15,23 @@\n #set $ref_file=\'\'\n \n #if $db\n- ln -s \'${db}\' \'${db.name}\' &&\n+ ln -sf \'${db}\' \'${db.name}\' &&\n #set $ref_file = $db.name\n #end if\n \n #if $primers[\'seqtype\'] == \'contig\'\n- ln -s \'${$primers.abi_input[\'forward\']}\' \'${primers.abi_input.name}_forward.ab1\' &&\n- ln -s \'${$primers.abi_input[\'reverse\']}\' \'${primers.abi_input.name}_reverse.ab1\' &&\n+ #set $forward_name=$primers.input.forward.name.rsplit(\'.\', 1)[0]\n+ #set $reverse_name=$primers.input.reverse.name.rsplit(\'.\', 1)[0]\n+ ln -sf \'${$primers.input[\'forward\']}\' \'${forward_name}_forward.${primers.input.forward.ext}\' &&\n+ ln -sf \'${$primers.input[\'reverse\']}\' \'${reverse_name}_reverse.${primers.input.reverse.ext}\' &&\n cryptogenotyper -i \'.\' -m \'$marker\' -t \'$primers.seqtype\' -f \'forward\' -r \'reverse\'\n #if $db\n --databasefile $ref_file\n #end if\n #else\n- ln -s \'${primers.abi_input}\' \'${primers.abi_input.element_identifier}\' &&\n- cryptogenotyper -i \'./${primers.abi_input.element_identifier}\' -m \'$marker\' -t \'$primers.seqtype\'\n+ #set $filename_no_ext=$primers.input.name.rsplit(\'.\', 1)[0]\n+ ln -sf \'${primers.input}\' \'${filename_no_ext}.${primers.input.ext}\' &&\n+ cryptogenotyper -i \'./${primers.input.name}\' -m \'$marker\' -t \'$primers.seqtype\'\n #if $db\n --databasefile $ref_file\n #end if\n@@ -39,57 +42,236 @@\n </command>\n <inputs>\n <param name="marker" type="select" label="Marker">\n- <option value="18S">SSU rRNA</option>\n+ <option value="18S">SSU rRNA (18S)</option>\n <option value="gp60">gp60</option>\n </param>\n <param name="db" type="data" optional="true" format="fasta" label="Reference Database File (optional):"/>\n <conditional name="primers">\n <param name="seqtype" type="select" label="Type of Sequences">\n- <option value="forward">Forward Only</option>\n+ <option value="forward" selected="true">Forward Only</option>\n <option value="reverse">Reverse Only</option>\n- <option selected="true" value="contig">Contig</option>\n+ <option value="contig">Contig</option>\n </param>\n <when value="contig">\n- <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)"/>\n+ <param name="input" type="data_collection" collection_type="paired" format="ab1,fasta" label="Paired Sequencing File(s)"/>\n </when>\n <when value="forward">\n- <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)"/>\n+ <param name="input" type="data" format="ab1,fasta" label="Forward Sequencing File(s)"/>\n </when>\n <when value="reverse">\n- <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)"/>\n+ <param name="input" type="data" format="ab1,fasta" label="Reverse Sequencing File(s)"/>\n </when>\n </conditional>\n+ <param name="show_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output run log?"></param>\n <param name="outputheader" type="boolean" truevalue="" falsevalue="--noheaderline" checked="true" label="Output header line in the report?">\n </param>\n \n \n </inputs>\n <outputs>\n- <data name="outfile" format="fasta" from_work_dir="result_cryptogenotyper_report.fa" label="${tool.name}:${on_string}:fastas"/>\n- <data name="outfile_report" format="tabular" from_work_dir="result_cryptogenotyper'..b'lement name="forward" value="test_illumina_gp60_F1.fasta"/>\n+ <element name="reverse" value="test_illumina_gp60_R1.fasta"/>\n+ </collection>\n+ </param>\n+ <output name="outfile_report_collection" ftype="tabular">\n+ <assert_contents>\n+ <has_text_matching expression="C.parvum"/>\n+ <has_text_matching expression="contig"/>\n+ <has_text_matching expression="IIaA16G3R1"/>\n+ <has_text_matching expression="IIaA15G2R2"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+\n+\n+ \n+\n </tests>\n \n \n@@ -98,30 +280,56 @@\n \n **Syntax**\n \n-CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers.\n-For more information please visit https://github.com/phac-nml/CryptoGenotyper.\n+CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA (18S) and gp60 markers.\n+\n+**\xe2\x9d\x97 Important:** To process **multiple input files** and generate **a single** combined report, please import and use the workflows available `here`_.\n+\n+.. _here: https://github.com/phac-nml/CryptoGenotyper/tree/main/CryptoGenotyper/GalaxyWorkflows\n+\n+\n+For a tutorial on how to use CryptoGenotyper, please refer to the `official tutorial`_.\n+\n+For more information, please visit https://github.com/phac-nml/CryptoGenotyper.\n+\n+.. _official tutorial: https://github.com/phac-nml/CryptoGenotyper/blob/docs/docs/CryptoGenotyperTutorial-CrownCopyright.pdf\n \n -----\n \n **Input:**\n \n-AB1 file(s) representing *Cryptosporidium\'s* SSU rRNA or gp60 locus (forward, reverse, or contig (forward and reverse paired-end reads)).\n-Optional: A custom reference database in .fa file format, to be used during the homology search for *Cryptosporidium* classification.\n+AB1 or FASTA file(s) representing Cryptosporidium\'s SSU rRNA (18S) or gp60 locus can be provided as single-end reads (either forward or reverse only) or as paired-end reads in contig mode (both a forward and a reverse read for each sample).\n+\n+Optional: A custom reference database of SSU rRNA or gp60 locus in .fasta file format, to be used during the homology search for *Cryptosporidium* classification.\n \n \n **Output:**\n \n-FASTA file containing the identification of the *Cryptosporidium* species/subtype and its corresponding sequence for each sample.\n+A tabular report and a FASTA file containing the identification of the *Cryptosporidium* species/subtype and its corresponding sequence for each sample along with other relevant details. \n+The gp60 subtyping is based on the `Deciphering a cryptic minefield: a guide to Cryptosporidium gp60 subtyping publication`_.\n+\n+.. _`Deciphering a cryptic minefield: a guide to Cryptosporidium gp60 subtyping publication`: https://doi.org/10.1016/j.crpvbd.2025.100257\n+\n </help>\n <citations>\n <citation type="bibtex">\n- @misc{githubCryptoGenotyper,\n- author = {Yanta C, Bessonov K, Robinson G, Troell K, Guy R},\n+ @ARTICLE{githubCryptoGenotyper,\n+ author = {Yanta, Christine A. and Bessonov, Kyrylo and Robinson, Guy and Troell, Karin and Guy, Rebecca A.},\n title = {CryptoGenotyper: a new bioinformatics tool to enhance Cryptosporidium identification},\n- publisher = {GitHub},\n- journal = {GitHub repository},\n- url = {https://github.com/phac-nml/CryptoGenotyper}\n+ journal = {Food and waterborne parasitology},\n+ year = {2021},\n+ volume = {23},\n+ url = {https://doi.org/10.1016/j.fawpar.2021.e00115}\n }</citation>\n+ <citation type="bibtex">\n+ @ARTICLE{RobinsonGp60,\n+ author = {Robinson, Gillian and Chalmers, Rachel M. and Elwin, Kirsty and Guy, Richard A. and Bessonov, Konstantin and Troell, Kristina and Xiao, Lihua},\n+ title = {Deciphering a cryptic minefield: A guide to Cryptosporidium gp60 subtyping},\n+ journal = {Current Research in Parasitology and Vector-Borne Diseases},\n+ year = {2025},\n+ volume = {7},\n+ url = {https://doi.org/10.1016/j.crpvbd.2025.100257}\n+ }\n+ }</citation>\n </citations>\n \n </tool>\n'

diff -r d4a96287909e -r a91455432cd4 test-data/test_illumina_18S_F.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_illumina_18S_F.fasta Fri Sep 12 18:50:40 2025 +0000

@@ -0,0 +1,8 @@
+>M04527:274:000000000-DBMY7:1:1102:16042:18930 1:N:0:20
+AGTGACAAGAAATAACAATACAGGACTTTTTGGTTTTGTAATTGGAATGAGTTAAGTATAAACCCCTTTACAAGTATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTTAATAATTTATATAAAATATTTTGATGAATATTTATATAATATTAACATAATTCATATTACTATTTTTTTTTT
+>M04527:274:000000000-DBMY7:1:1101:20679:16373 1:N:0:20
+AGTGACAAGAAATAACAATACAGGACTTTTTGGTTTTGTAATTGGAATGAGTTAAGTATAAACCCCTTTACAAGTATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTTAATAATTTATATAAAATATTTTGATGAATATTTATATAATATTAACATAATTCATATTACTATTTTTTTTTT
+>M04527:274:000000000-DBMY7:1:1102:12557:11653 1:N:0:20
+AGTGACAAGAAATAACAATACAGGACTTTTTGGTTTTGTAATTGGAATGAGTTAAGTATAAACCCCTTTACAAGTATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTTAATAATTTATATAAAATATTTTGATGAATATTTATATAATATTAACATAATTCATATTACTATTTTTTTTAG
+>M04527:274:000000000-DBMY7:1:1102:17887:8992 1:N:0:20
+AGTGACAAGAAATAACAATACAGGACTTTTTGGTTTTGTAATTGGAATGAGTTAAGTATAAACCCCTTTACAAGTATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTTAATAATTTATATAAAATATTTTGATGAATATTTATATAATATTAACATAATTCATATTACTATTTTTTTTTT

diff -r d4a96287909e -r a91455432cd4 test-data/test_illumina_18S_R.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_illumina_18S_R.fasta Fri Sep 12 18:50:40 2025 +0000

diff -r d4a96287909e -r a91455432cd4 test-data/test_illumina_gp60_F1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_illumina_gp60_F1.fasta Fri Sep 12 18:50:40 2025 +0000

@@ -0,0 +1,5 @@
+>M04527:274:000000000-DBMY7:1:1102:14324:28396 1:N:0:26
+TCCGCTGTATTCTCAGCCCCAGCCGTTCCACTCAGAGGAACTTTAAAGGATGTTCCTGTTGAGGGCTCATCATCGTCATCGTCATCGTCATCATCATCATCATCATCATCATCATCATCATCAACATCAACCGTCGCACCAGCAAATAAGGCAAGAACTGGAGAAGACGCAGAAGGCAGTCAAGATTCTAGTGGTACTGAAGCTTCTGGTAGCCAGGGTTCTGAAGAGGAAGGTAGTGAAGACGATGGCCA
+>M04527:274:000000000-DBMY7:1:1102:20035:28200 1:N:0:26
+TCCGCTGTATTCTCAGCCCCTGCCGTTCCACTCAGAGGAACTTTAAAGGATGTTCCTGTTGAGGGCTCATCATCGTCATCGTCATCATCATCATCATCATCATCATCATCATCATCAACATCAACATCAACCGTCGCACCAGCAAATAAGGCAAGAACTGGAGAAGACGCAGAAGGCAGTCAAGATTCTAGTGGTACTGAAGCTTCTGGTAGCCAGGGTTCTGAAGAGGAAGGTAGTGAAGACGATGGCCA
+

diff -r d4a96287909e -r a91455432cd4 test-data/test_illumina_gp60_R1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_illumina_gp60_R1.fasta Fri Sep 12 18:50:40 2025 +0000

@@ -0,0 +1,4 @@
+>M04527:274:000000000-DBMY7:1:1102:14324:28396 2:N:0:26
+CGAACCACATTACAAATGAAGTGCCGCATTCTTCTTTTGGAGTAGCTTCTATGGTTTCGGTAGTTGCGCCTTCACTTTGAGCTGGAGTAGTGGGTTGGGAAGCAGCACTAGTTTGGCCATCGTCTTCACTACCTTCCTCTTCAGAACCCTGGCTACCAGAAGCTTCAGTACCACTAGAATCTTGACTGCCTTCTGCGTCTTCTCCAGTTCTTGCCTTATTTGCTGGTGCGACGGTTGATGTTGATGATGAT
+>M04527:274:000000000-DBMY7:1:1102:20035:28200 2:N:0:26
+CGAACCACATTACAAATGAAGTGCCGCATTCTTCTTTTGGAGTAGCTTCTATGGTTTCGGTAGTTGCGCCTTCACTTTGAGCTGGAGTAGTGGGTTGGGAAGCAGCACTAGTTTGGCCATCGTCTTCACTACCTTCCTCTTCAGAACCCTGGCTACCAGAAGCTTCAGTACCACTAGAATCTTGACTGCCTTCTGCGTCTTCTCCAGTTCTTGCCTTATTTGCTGGTGCGACGGTTGATGTTGATGTTGAT
\ No newline at end of file