| Previous changeset 3:5cecae70d439 (2017-07-12) Next changeset 5:6a17e1229b9f (2020-08-13) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2 commit 04c75332ac618b43ce5c3f307f7866e97147e865 |
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modified:
mirdeep2.xml |
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added:
test-data/detailed_fasta/known_mature.fa test-data/detailed_fasta/known_pres.fa test-data/detailed_fasta/known_star.fa test-data/detailed_fasta/not_mature.fa test-data/detailed_fasta/not_pres.fa test-data/detailed_fasta/not_star.fa test-data/detailed_fasta/novel_mature.fa test-data/detailed_fasta/novel_pres.fa test-data/detailed_fasta/novel_star.fa |
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removed:
miRDeep2.tar.gz |
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| diff -r 5cecae70d439 -r d338dbd76ea0 miRDeep2.tar.gz |
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| Binary file miRDeep2.tar.gz has changed |
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| diff -r 5cecae70d439 -r d338dbd76ea0 mirdeep2.xml --- a/mirdeep2.xml Wed Jul 12 14:37:54 2017 -0400 +++ b/mirdeep2.xml Thu Apr 05 08:37:10 2018 -0400 |
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| b'@@ -1,80 +1,67 @@\n-<tool id="rbc_mirdeep2" name="MiRDeep2" version="2.0.0">\n+<tool id="rbc_mirdeep2" name="MiRDeep2" version="2.0.0.8.1">\n <description>identification of novel and known miRNAs</description>\n <requirements>\n <requirement type="package" version="2.0.0.8">mirdeep2</requirement>\n </requirements>\n- <stdio>\n- <!-- Anything other than zero is an error -->\n- <exit_code range="1:" />\n- <exit_code range=":-1" />\n- <!-- In case the return code has not been set propery check stderr too -->\n- <regex match="Error:" />\n- <regex match="Exception:" />\n- </stdio>\n- <command>\n+ <command detect_errors="aggressive">\n <![CDATA[\n miRDeep2.pl\n- \n+\n $reads\n $genome\n $mappings\n- \n+\n #if $mature_this\n $mature_this\n #else\n none\n #end if\n- \n+\n #if $mature_other\n $mature_other\n #else\n none\n #end if\n- \n+\n #if $precursors\n $precursors\n #else\n none\n #end if\n- \n+\n #if $species.value != \'all\'\n -t $species\n #end if\n- \n+\n #if $star_sequences\n -s $star_sequences\n #end if\n- \n+\n #if $min_read_stack\n -a $min_read_stack\n #end if\n- \n+\n #if $min_read_stack\n -a $min_read_stack\n #end if\n- \n+\n -g $max_precursors_analyze\n -b $min_score_cutoff\n $disable_randfold\n- \n- ; mv result*.bed result.bed 2> /dev/null\n- ; mv result*.csv result.csv 2> /dev/null\n- ; mv mirdeep_runs/run*/output.mrd . 2> /dev/null\n- ; mv mirdeep_runs/run*/survey.csv . 2> /dev/null\n- \n+\n+ &&\n+\n ## html output\n- ;\n mv result*.html $html 2> /dev/null\n- \n+\n ## move pdf directory to be accessible from the new index.html\n- ;\n+ &&\n mkdir -p $html.files_path 2> /dev/null\n- ;\n+ &&\n mv pdfs* $html.files_path 2> /dev/null\n- \n ]]>\n </command>\n- <inputs> \n+ <inputs>\n <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads">\n <help>\n <![CDATA[\n@@ -86,7 +73,7 @@\n </param>\n <param name="genome" format="fasta" type="data" label="Genome" help="Genome contigs in fasta format. The identifiers should be unique."/>\n <param name="mappings" format="tabular" type="data" label="Mappings" help="Reads mapped against genome. Mappings should be in ARF format."/>\n- <param name="mature_this" optional="true" format="fasta" type="data" label="Mature miRNA sequences for this species" \n+ <param name="mature_this" optional="true" format="fasta" type="data" label="Mature miRNA sequences for this species"\n help="miRBase miRNA sequences in fasta format. These should be the known mature sequences for the species being analyzed."/>\n <param name="mature_other" optional="true" format="fasta" type="data" label="Mature miRNA sequences for related species">\n <help>\n@@ -96,9 +83,9 @@\n ]]>\n </help>\n </param>\n- <param name="precursors" optional="true" format="fasta" type="data" label="Precursor sequences" \n+ <param name="precursors" optional="true" format="fasta" type="data" label="Precursor sequences"\n help="miRBase miRNA precursor sequences in fasta format. These should be the known precursor sequences for the species being analyzed."/>\n- \n+\n <param name="species" type="select" label="Search in species" help="If not searching in a specific species all species in your files will be analyzed. (-t)">\n <option value="all">All species</option>\n <option value="tni">tetraodon</option>\n@@ -134,7 +121,7 @@\n <option value="dsi">d.simulans</option>\n </param>\n <param name="star_sequences" format="fasta" type="data" optional="true" label="Star sequences" help="From miRBase in fasta format (optional) (-s)"/>\n- \n+\n <param name="min_read_stack" optional="true" t'..b'ults_*/known_pres_*.fa" label="${tool.name} on ${on_string}: known precursors">\n+ <filter>detailed_fasta</filter>\n+ </data>\n+ <data name="known_star" format="fasta" from_work_dir="mirna_results_*/known_star_*.fa" label="${tool.name} on ${on_string}: known star">\n+ <filter>detailed_fasta</filter>\n+ </data>\n+ <data name="not_mature" format="fasta" from_work_dir="mirna_results_*/not_mature_*.fa" label="${tool.name} on ${on_string}: not detected mature">\n+ <filter>detailed_fasta</filter>\n+ </data>\n+ <data name="not_pres" format="fasta" from_work_dir="mirna_results_*/not_pres_*.fa" label="${tool.name} on ${on_string}: not detected precursors">\n+ <filter>detailed_fasta</filter>\n+ </data>\n+ <data name="not_star" format="fasta" from_work_dir="mirna_results_*/not_star_*.fa" label="${tool.name} on ${on_string}: not detected star">\n+ <filter>detailed_fasta</filter>\n+ </data>\n+ <data name="novel_mature" format="fasta" from_work_dir="mirna_results_*/novel_mature_*.fa" label="${tool.name} on ${on_string}: novel mature">\n+ <filter>detailed_fasta</filter>\n+ </data>\n+ <data name="novel_pres" format="fasta" from_work_dir="mirna_results_*/novel_pres_*.fa" label="${tool.name} on ${on_string}: novel precursors">\n+ <filter>detailed_fasta</filter>\n+ </data>\n+ <data name="novel_star" format="fasta" from_work_dir="mirna_results_*/novel_star_*.fa" label="${tool.name} on ${on_string}: novel star">\n+ <filter>detailed_fasta</filter>\n+ </data>\n </outputs>\n <tests>\n <test>\n@@ -164,12 +180,36 @@\n <param name="mature_this" value="mature_ref_this_species.fa"/>\n <param name="mature_other" value="mature_ref_other_species.fa"/>\n <param name="precursors" value="precursors_ref_this_species.fa"/>\n- \n+\n <output name="tab_results" file="result.csv" compare="sim_size"/>\n <output name="pred_acc" file="survey.csv" compare="sim_size"/>\n <output name="bed_out" file="result.bed" compare="sim_size"/>\n <output name="mrd_out" file="output.mrd" compare="sim_size"/>\n </test>\n+ <test>\n+ <param name="reads" value="reads_collapsed.fa"/>\n+ <param name="genome" value="cel_cluster.fa"/>\n+ <param name="mappings" value="reads_collapsed_vs_genome.arf"/>\n+ <param name="mature_this" value="mature_ref_this_species.fa"/>\n+ <param name="mature_other" value="mature_ref_other_species.fa"/>\n+ <param name="precursors" value="precursors_ref_this_species.fa"/>\n+ <param name="detailed_fasta" value="true"/>\n+\n+ <output name="tab_results" file="result.csv" compare="sim_size"/>\n+ <output name="pred_acc" file="survey.csv" compare="sim_size"/>\n+ <output name="bed_out" file="result.bed" compare="sim_size"/>\n+ <output name="mrd_out" file="output.mrd" compare="sim_size"/>\n+\n+ <output name="known_mature" file="detailed_fasta/known_mature.fa" compare="sim_size"/>\n+ <output name="known_pres" file="detailed_fasta/known_pres.fa" compare="sim_size"/>\n+ <output name="known_star" file="detailed_fasta/known_star.fa" compare="sim_size"/>\n+ <output name="not_mature" file="detailed_fasta/not_mature.fa" compare="sim_size"/>\n+ <output name="not_pres" file="detailed_fasta/not_pres.fa" compare="sim_size"/>\n+ <output name="not_star" file="detailed_fasta/not_star.fa" compare="sim_size"/>\n+ <output name="novel_mature" file="detailed_fasta/novel_mature.fa" compare="sim_size"/>\n+ <output name="novel_pres" file="detailed_fasta/novel_pres.fa" compare="sim_size"/>\n+ <output name="novel_star" file="detailed_fasta/novel_star.fa" compare="sim_size"/>\n+ </test>\n </tests>\n <help>\n <![CDATA[\n' |
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| diff -r 5cecae70d439 -r d338dbd76ea0 test-data/detailed_fasta/known_mature.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/detailed_fasta/known_mature.fa Thu Apr 05 08:37:10 2018 -0400 |
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| @@ -0,0 +1,14 @@ +>chrII:11534525-11540624_11 +TCACCGGGTGAACACTTGCAGT +>chrII:11534525-11540624_17 +TCACCGGGTGTACATCAGCTAA +>chrII:11534525-11540624_9 +TCACCGGGTGAAAATTCGCATG +>chrII:11534525-11540624_15 +TCACCGGGTGTAAATCAGCTTG +>chrII:11534525-11540624_19 +GGTGGTTTTTCTCTGCAGTGATA +>chrII:11534525-11540624_13 +TCACCGGGAGAAAAACTGGAGT +>chrII:11534525-11540624_12 +TCACCGGGTGAACACTTGCAGT |
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| diff -r 5cecae70d439 -r d338dbd76ea0 test-data/detailed_fasta/known_pres.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/detailed_fasta/known_pres.fa Thu Apr 05 08:37:10 2018 -0400 |
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| @@ -0,0 +1,14 @@ +>chrII:11534525-11540624_11 +TGTGGGTGTCCGTTGCGGTGCTACATTCTCTAATCTGTATCACCGGGTGAACACTTGCAGT +>chrII:11534525-11540624_17 +AGTGGATGTATGCCATGATGATAAGATATCAGAAATCCTATCACCGGGTGTACATCAGCTAA +>chrII:11534525-11540624_9 +CGCCAATTTTCGCTTCAGTGCTAGACCATCCAAAGTGTCTATCACCGGGTGAAAATTCGCATG +>chrII:11534525-11540624_15 +AGCTGATTTCGTCTTGGTAATAAGCTCGTCATTGAGATTATCACCGGGTGTAAATCAGCTTG +>chrII:11534525-11540624_19 +GGTGGTTTTTCTCTGCAGTGATAGATACTTCTAACAACTCGCTATCACCGGGTGAAAAATCACCTA +>chrII:11534525-11540624_13 +TCCGGTTTTTTCCGTGGTGATAACGCATCCAAAAGTCTCTATCACCGGGAGAAAAACTGGAGT +>chrII:11534525-11540624_12 +TCACCGGGTGAACACTTGCAGTGGTCCTCGTGGTTTCTCTGTGAGCCAGGTCCTGTTCCGGTTTTTTCCGTGGTGATA |
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| diff -r 5cecae70d439 -r d338dbd76ea0 test-data/detailed_fasta/known_star.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/detailed_fasta/known_star.fa Thu Apr 05 08:37:10 2018 -0400 |
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| @@ -0,0 +1,14 @@ +>chrII:11534525-11540624_11 +TGTGGGTGTCCGTTGCGGTGCTA +>chrII:11534525-11540624_17 +AGTGGATGTATGCCATGATGATA +>chrII:11534525-11540624_9 +CGCCAATTTTCGCTTCAGTGCTA +>chrII:11534525-11540624_15 +AGCTGATTTCGTCTTGGTAATA +>chrII:11534525-11540624_19 +TCACCGGGTGAAAAATCACCTA +>chrII:11534525-11540624_13 +TCCGGTTTTTTCCGTGGTGATA +>chrII:11534525-11540624_12 +TGTTCCGGTTTTTTCCGTGGTGATA |
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| diff -r 5cecae70d439 -r d338dbd76ea0 test-data/detailed_fasta/novel_mature.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/detailed_fasta/novel_mature.fa Thu Apr 05 08:37:10 2018 -0400 |
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| @@ -0,0 +1,2 @@ +>chrII:11534525-11540624_7 +TCACCGGGTGGAAACTAGCAGT |
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| diff -r 5cecae70d439 -r d338dbd76ea0 test-data/detailed_fasta/novel_pres.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/detailed_fasta/novel_pres.fa Thu Apr 05 08:37:10 2018 -0400 |
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| @@ -0,0 +1,2 @@ +>chrII:11534525-11540624_7 +TGCTGGTTTCTTCCACAGTGGTACTTTCCATTAGAACTATCACCGGGTGGAAACTAGCAGT |
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| diff -r 5cecae70d439 -r d338dbd76ea0 test-data/detailed_fasta/novel_star.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/detailed_fasta/novel_star.fa Thu Apr 05 08:37:10 2018 -0400 |
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| @@ -0,0 +1,2 @@ +>chrII:11534525-11540624_7 +TGCTGGTTTCTTCCACAGTGGTA |