Mercurial > repos > gga > genenotebook_genenotebook_build
changeset 4:ace14a8ac6e4 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 81226a2f347b2dc273546311e7269c07f0b0f485
| author | gga |
|---|---|
| date | Tue, 10 Oct 2023 15:29:02 +0000 |
| parents | 1d59e907fa98 |
| children | bd94e502872a |
| files | genenotebook_build.xml macros.xml test-data/exp.tsv test-data/hectar.tsv |
| diffstat | 4 files changed, 37 insertions(+), 20 deletions(-) [+] |
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--- a/genenotebook_build.xml Wed Sep 20 16:48:06 2023 +0000 +++ b/genenotebook_build.xml Tue Oct 10 15:29:02 2023 +0000 @@ -40,6 +40,10 @@ genoboo add eggnog @CONNECT_INFO@ '${annot.eggnog}'; #end if + #if $annot.hectar: + genoboo add hectar @CONNECT_INFO@ '${annot.hectar}'; + #end if + #if $annot.blast_cond.blast_choice == "blast": genoboo add blast @CONNECT_INFO@ --format 'xml' @@ -57,11 +61,15 @@ #end if #for exp in $annot.expression: - genoboo add transcriptome @CONNECT_INFO@ - --sample-name '${exp.sample_name}' - --replica-group '${exp.replica_group}' - --sample-description '${exp.sample_description}' - '${exp.counts}'; + genoboo add expression @CONNECT_INFO@ + --sample-description '' + ${exp.public} + #for replica in $exp.expression_replicas: + --replicas '${replica.replicas}' + --replica-names '${replica.replica_names}' + #end for + -- + '${exp.counts}'; #end for #end for #end for @@ -97,6 +105,7 @@ </conditional> <param name="interproscan" label="InterProScan results" optional="true" type="data" format="tsv,gff3" /> <param name="eggnog" label="EggNOG-Mapper results" optional="true" type="data" format="tsv" /> + <param name="hectar" label="Hectar results" optional="true" type="data" format="tsv" /> <conditional name="blast_cond"> <param name="blast_choice" type="select" label="Import Blast or Diamond results"> @@ -120,10 +129,12 @@ </conditional> <repeat name="expression" title="Expression data"> - <param name="counts" label="Expression data" optional="true" type="data" format="tsv" /> - <param argument="--sample-name" name="sample_name" label="Unique sample name" type="text" /> - <param argument="--replica-group" name="replica_group" label="Identifier to group samples that belong to the same experiment" type="text" /> - <param argument="--sample-description" name="sample_description" label="Description of the experiment" type="text" /> + <param name="counts" label="Expression data tabular file" help="One line per mRNA, first column is mRNA ID, each other columns is an experimental condition. TPM values preferably." optional="false" type="data" format="tsv" /> + <param name="public" label="Public access" type="boolean" truevalue="--public" falsevalue="" value="false" /> + <repeat name="expression_replicas" title="Expression replicas"> + <param argument="--replica-names" label="Name of a replica group" type="text"/> + <param argument="--replicas" label="Comma-separated list of columns of replicas (e.g. 1,2,3)" type="text" help="Comma-separated list of column positions, which are part of the same replica group. Columns not mentionned in any replica group will be considered to be a single replica experiment." /> + </repeat> </repeat> </repeat> </repeat> @@ -202,6 +213,7 @@ <param name="annotation" value="annot.gff" /> <param name="interproscan" value="interproscan.tsv" ftype="tsv" /> <param name="eggnog" value="eggnog.tsv" ftype="tsv" /> + <param name="hectar" value="hectar.tsv" ftype="tsv" /> </repeat> </repeat> <output name="gnb_db" file="output/genome_annot_ips_en.tar.bz2" compare="sim_size" delta="15000" /> @@ -235,9 +247,7 @@ <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" /> + <param name="public" value="true" /> </repeat> </repeat> </repeat> @@ -246,7 +256,7 @@ <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" /> + <has_text text="addExpression succesfully inserted 4 elements" /> </assert_stdout> </test> <test> @@ -272,9 +282,14 @@ <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 name="expression_replicas"> + <param name="replicas" value="1,2" /> + <param name="replica_names" value="ReplicaName1" /> + </repeat> + <repeat name="expression_replicas"> + <param name="replicas" value="3,4" /> + <param name="replica_names" value="ReplicaName2" /> + </repeat> </repeat> </repeat> </repeat> @@ -283,7 +298,7 @@ <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" /> + <has_text text="addExpression succesfully inserted 4 elements" /> </assert_stdout> </test> </tests>
--- a/macros.xml Wed Sep 20 16:48:06 2023 +0000 +++ b/macros.xml Tue Oct 10 15:29:02 2023 +0000 @@ -7,7 +7,7 @@ </requirements> </xml> - <token name="@TOOL_VERSION@">0.4.5</token> + <token name="@TOOL_VERSION@">0.4.7</token> <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> <xml name="citation">
--- a/test-data/exp.tsv Wed Sep 20 16:48:06 2023 +0000 +++ b/test-data/exp.tsv Tue Oct 10 15:29:02 2023 +0000 @@ -1,2 +1,2 @@ -target_id length eff_length est_counts tpm -MMUCEDO_000001-T1 1221 1021.99 21 1.80368 +gene Sample1 Sample2 Sample3 Sample4 +MMUCEDO_000001-T1 1000 2000 3000 4000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hectar.tsv Tue Oct 10 15:29:02 2023 +0000 @@ -0,0 +1,2 @@ +protein id predicted targeting category signal peptide score signal peptide cleavage site type II signal anchor score chloroplast score mitochondrion score other score +MMUCEDO_000002-T1 other localisation 0.0583 - 0.0228 - 0.1032 0.8968