Mercurial > repos > gga > genenotebook_genenotebook_build
changeset 2:5a6050937cb9 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit ec3c633a0751bb9e253bcd77fea425180c9a0014
| author | gga |
|---|---|
| date | Fri, 14 Apr 2023 10:13:56 +0000 |
| parents | f415e44e71de |
| children | 1d59e907fa98 |
| files | genenotebook_build.xml kill_gnb.sh launch_gnb.sh macros.xml test-data/output/genome.tar.bz2 test-data/output/genome_annot.tar.bz2 test-data/output/genome_annot_ips.tar.bz2 test-data/output/genome_annot_ips_en.tar.bz2 test-data/output/genome_annot_ips_en_bl_exp.tar.bz2 test-data/output/genome_reload.tar.bz2 |
| diffstat | 10 files changed, 67 insertions(+), 9 deletions(-) [+] |
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--- a/genenotebook_build.xml Mon Apr 03 15:01:52 2023 +0000 +++ b/genenotebook_build.xml Fri Apr 14 10:13:56 2023 +0000 @@ -5,7 +5,7 @@ <import>macros.xml</import> </macros> <expand macro="requirements" /> - <command detect_errors="aggressive"><![CDATA[ + <command detect_errors="exit_code"><![CDATA[ @START_GNB@ #for genome in $genomes: @@ -40,13 +40,20 @@ genoboo add eggnog @CONNECT_INFO@ '${annot.eggnog}'; #end if - #if $annot.blast_cond.blast_choice == "yes": + #if $annot.blast_cond.blast_choice == "blast": genoboo add blast @CONNECT_INFO@ --format 'xml' --algorithm '${annot.blast_cond.algorithm}' --matrix '${annot.blast_cond.matrix}' --database '${annot.blast_cond.database}' '${annot.blast_cond.blast}'; + #elif $annot.blast_cond.blast_choice == "diamond": + genoboo add diamond @CONNECT_INFO@ + --format 'xml' + --algorithm '${annot.blast_cond.algorithm}' + --matrix '${annot.blast_cond.matrix}' + --database '${annot.blast_cond.database}' + '${annot.blast_cond.diamond}'; #end if #for exp in $annot.expression: @@ -94,11 +101,18 @@ <conditional name="blast_cond"> <param name="blast_choice" type="select" label="Import Blast or Diamond results"> <option value="no" selected="true">No</option> - <option value="yes">Yes</option> + <option value="blast">Blast</option> + <option value="diamond">Diamond</option> </param> <when value="no" /> - <when value="yes"> - <param name="blast" label="Blast or Diamond results" optional="false" type="data" format="xml" /> + <when value="blast"> + <param name="blast" label="Blast results (xml)" optional="false" type="data" format="xml" /> + <param argument="--algorithm" label="Algorithm" optional="false" type="text" help="e.g. blastx, blastp" /> + <param argument="--matrix" label="Matrix" optional="false" type="text" help="e.g. BLOSUM90, BLOSUM80, PAM100" /> + <param argument="--database" label="database" optional="false" type="text" help="e.g. Non-reundant protein sequences (nr)" /> + </when> + <when value="diamond"> + <param name="diamond" label="Diamond results (xml)" optional="false" type="data" format="xml" /> <param argument="--algorithm" label="Algorithm" optional="false" type="text" help="e.g. blastx, blastp" /> <param argument="--matrix" label="Matrix" optional="false" type="text" help="e.g. BLOSUM90, BLOSUM80, PAM100" /> <param argument="--database" label="database" optional="false" type="text" help="e.g. Non-reundant protein sequences (nr)" /> @@ -166,7 +180,7 @@ <assert_stdout> <has_text text="addGenome succesfully inserted 1 elements" /> <has_text text="addAnnotation succesfully inserted 5 elements" /> - <has_text text="addInterproscan succesfully inserted 5 elements" /> + <has_text text="addInterproscan succesfully inserted 3 elements" /> </assert_stdout> </test> <test> @@ -194,7 +208,7 @@ <assert_stdout> <has_text text="addGenome succesfully inserted 1 elements" /> <has_text text="addAnnotation succesfully inserted 5 elements" /> - <has_text text="addInterproscan succesfully inserted 5 elements" /> + <has_text text="addInterproscan succesfully inserted 3 elements" /> <has_text text="addEggnog succesfully inserted 4 elements" /> </assert_stdout> </test> @@ -212,7 +226,7 @@ </conditional> <conditional name="blast_cond"> - <param name="blast_choice" value="yes"/> + <param name="blast_choice" value="blast"/> <param name="blast" value="blast.xml" ftype="xml" /> <param name="algorithm" value="blastx" /> <param name="matrix" value="BLOSUM80" /> @@ -235,6 +249,43 @@ <has_text text="addTranscriptome succesfully inserted 1 elements" /> </assert_stdout> </test> + <test> + <repeat name="genomes"> + <param name="name" value="Test org 2" /> + <param name="genome" value="genome.fa" /> + <repeat name="annots"> + <param name="annotation" value="annot.gff" /> + + <conditional name="prot_naming"> + <param name="method" value="regex"/> + <param name="re_protein_capture" value="^(.*?)-T([0-9]+)$" /> + <param name="re_protein" value="$1-P$2" /> + </conditional> + + <conditional name="blast_cond"> + <param name="blast_choice" value="diamond"/> + <param name="diamond" value="blast.xml" ftype="xml" /> + <param name="algorithm" value="blastx" /> + <param name="matrix" value="BLOSUM62" /> + <param name="database" value="Non-reundant garbage (nrg)" /> + </conditional> + + <repeat name="expression"> + <param name="counts" value="exp.tsv" ftype="tsv" /> + <param name="sample_name" value="Sample1_rep1" /> + <param name="replica_group" value="Sample1" /> + <param name="sample_description" value="Pointless experiment" /> + </repeat> + </repeat> + </repeat> + <output name="gnb_db" file="output/genome_annot_ips_en_bl_exp.tar.bz2" compare="sim_size" delta="15000" /> + <assert_stdout> + <has_text text="addGenome succesfully inserted 1 elements" /> + <has_text text="addAnnotation succesfully inserted 5 elements" /> + <has_text text="addSimilarSequence succesfully inserted 1 elements" /> + <has_text text="addTranscriptome succesfully inserted 1 elements" /> + </assert_stdout> + </test> </tests> <help><![CDATA[ Build a GeneNoteBook by loading data into a MongoDB database. The resulting dataset can then be displayed with the "View a GeneNoteBook" interactive tool (to be written).
--- a/kill_gnb.sh Mon Apr 03 15:01:52 2023 +0000 +++ b/kill_gnb.sh Fri Apr 14 10:13:56 2023 +0000 @@ -3,6 +3,11 @@ # Make sure everything is cleaned (including job queue) sleep 5 +# Print server log +echo "" +echo "--- 'genoboo run' stopped, printing logs (server side) ---" +cat ./gnb.log + # Kill GeneNoteBook kill $GNB_PID
--- a/launch_gnb.sh Mon Apr 03 15:01:52 2023 +0000 +++ b/launch_gnb.sh Fri Apr 14 10:13:56 2023 +0000 @@ -17,6 +17,8 @@ TMP_STORAGE=$(pwd)/tmp_storage mkdir "$TMP_STORAGE" +export NODE_OPTIONS="--max-old-space-size=$((${GALAXY_MEMORY_MB:-8192} * 75 / 100))" + genoboo run --storage-path "$TMP_STORAGE" --port ${GNB_PORT} --mongo-url mongodb://$MONGO_URI%2Fmongodb-27017.sock/genenotebook > ./gnb.log 2>&1 & export GNB_PID=$!
--- a/macros.xml Mon Apr 03 15:01:52 2023 +0000 +++ b/macros.xml Fri Apr 14 10:13:56 2023 +0000 @@ -7,7 +7,7 @@ </requirements> </xml> - <token name="@TOOL_VERSION@">0.4.1</token> + <token name="@TOOL_VERSION@">0.4.2</token> <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> <xml name="citation">