Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Genenotebook 0.4.7 #85

Merged
merged 8 commits into from
Oct 10, 2023
Merged

Genenotebook 0.4.7 #85

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
235ea8a
expression (1/?)
mboudet Sep 26, 2023
72a16c1
fix
mboudet Sep 29, 2023
6bd9e29
more test
mboudet Oct 2, 2023
57e1639
Merge repeat block
mboudet Oct 2, 2023
ac27e5e
typo
mboudet Oct 2, 2023
4b15c1c
polish
abretaud Oct 10, 2023
ec665a0
add hectar (fixes #84)
abretaud Oct 10, 2023
b182dcc
test for hectar
abretaud Oct 10, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
49 changes: 32 additions & 17 deletions tools/genenotebook/genenotebook_build.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand All @@ -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
Expand Down Expand Up @@ -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">
Expand All @@ -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>
Expand Down Expand Up @@ -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" />
Expand Down Expand Up @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand Down
2 changes: 1 addition & 1 deletion tools/genenotebook/macros.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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">
Expand Down
4 changes: 2 additions & 2 deletions tools/genenotebook/test-data/exp.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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
2 changes: 2 additions & 0 deletions tools/genenotebook/test-data/hectar.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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