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

Fix glimmer tools error handling #6641

Merged
merged 3 commits into from
Dec 16, 2024
Merged

Fix glimmer tools error handling #6641

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
b8c8831
Fix glimmer tools error handling
mvdbeek Dec 16, 2024
527bd08
Add on_string
bernt-matthias Dec 16, 2024
2ce8adf
Bump version and use standard tokens
mvdbeek Dec 16, 2024
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
4 changes: 0 additions & 4 deletions tools/glimmer/.lint_skip
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1 @@
CommandTODO
InputsBoolDistinctValues
OutputsLabelDuplicatedNoFilter
TestsExpectNumOutputs
XMLOrder
4 changes: 2 additions & 2 deletions tools/glimmer/glimmer_acgt_content.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<tool id="glimmer_acgt_content" name="ACGT Content" version="@WRAPPER_VERSION@">
<tool id="glimmer_acgt_content" name="ACGT Content" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
<description>of windows in each sequence</description>
<expand macro="bio_tools"/>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="bio_tools"/>
<expand macro="requirements"/>
<command><![CDATA[
window-acgt
Expand Down
4 changes: 2 additions & 2 deletions tools/glimmer/glimmer_build_icm.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<tool id="glimmer_build_icm" name="Glimmer ICM builder" version="@WRAPPER_VERSION@">
<tool id="glimmer_build_icm" name="Glimmer ICM builder" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
<description></description>
<expand macro="bio_tools"/>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="bio_tools"/>
<expand macro="requirements"/>
<command><![CDATA[
build-icm
Expand Down
4 changes: 2 additions & 2 deletions tools/glimmer/glimmer_extract.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<tool id="glimmer_extract" name="Extract sequence regions" version="@WRAPPER_VERSION@">
<tool id="glimmer_extract" name="Extract sequence regions" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
<description>from a genome</description>
<expand macro="bio_tools"/>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="bio_tools"/>
<expand macro="requirements"/>
<command><![CDATA[
extract
Expand Down
8 changes: 4 additions & 4 deletions tools/glimmer/glimmer_gbk_to_orf.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<tool id="glimmer_gbk_to_orf" name="Extract ORF" version="@WRAPPER_VERSION@">
<tool id="glimmer_gbk_to_orf" name="Extract ORF" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
<description>from a GenBank file</description>
<expand macro="bio_tools"/>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="bio_tools"/>
<expand macro="requirements"/>
<command><![CDATA[
python '$__tool_directory__/glimmer_gbk_to_orf.py'
Expand All @@ -16,8 +16,8 @@
<param name="infile" type='data' format="genbank" label="gene bank file"/>
</inputs>
<outputs>
<data name="aa_output" format="fasta" />
<data name="nc_output" format="fasta" />
<data name="aa_output" format="fasta" label="${tool.name} on ${on_string}: Amino acids"/>
<data name="nc_output" format="fasta" label="{tool.name} on ${on_string}: Nucleotides"/>
</outputs>
<tests>
<test>
Expand Down
4 changes: 2 additions & 2 deletions tools/glimmer/glimmer_glimmer_to_gff.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<tool id="glimmer_glimmer_to_gff" name="Convert Glimmer to GFF" version="@WRAPPER_VERSION@+galaxy1">
<tool id="glimmer_glimmer_to_gff" name="Convert Glimmer to GFF" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
<description></description>
<expand macro="bio_tools"/>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="bio_tools"/>
<expand macro="requirements"/>
<command><![CDATA[
python '$__tool_directory__/glimmer_glimmer_to_gff.py'
Expand Down
4 changes: 2 additions & 2 deletions tools/glimmer/glimmer_long_orfs.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<tool id="glimmer_long_orfs" name="Glimmer long ORFs" version="@WRAPPER_VERSION@">
<tool id="glimmer_long_orfs" name="Glimmer long ORFs" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
<description>identify long, non-overlapping ORFs</description>
<expand macro="bio_tools"/>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="bio_tools"/>
<expand macro="requirements"/>
<command><![CDATA[
long-orfs
Expand Down
28 changes: 21 additions & 7 deletions tools/glimmer/glimmer_w_icm.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<tool id="glimmer_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@">
<tool id="glimmer_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
<description>Predict ORFs in prokaryotic genomes (knowlegde-based)</description>
<expand macro="bio_tools"/>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="bio_tools"/>
<expand macro="requirements"/>
<command detect_errors="aggressive"><![CDATA[
glimmer3
Expand Down Expand Up @@ -87,20 +87,20 @@
</when>
</conditional>

<param name="report" type="boolean" truevalue="" falsevalue="" checked="false" label="Report the classic glimmer table output"/>
<param name="detailed_report" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a detailed gene prediction report as separate file"/>
<param name="report" type="boolean" checked="false" label="Report the classic glimmer table output"/>
<param name="detailed_report" type="boolean" checked="false" label="Output a detailed gene prediction report as separate file"/>
</inputs>
<outputs>
<data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" />
<data name="report_output" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)">
<filter>report == True</filter>
<filter>report</filter>
</data>
<data name="detailed_output" format="txt" label="Glimmer3 on ${on_string} (detailed report)">
<filter>detailed_report == True</filter>
<filter>detailed_report</filter>
</data>
</outputs>
<tests>
<test>
<test expect_num_outputs="3">
<param name="seq_input" value='streptomyces_Tue6071_plasmid_genomic.fasta' />
<param name="icm_input" value='streptomyces_Tu6071_plasmid_genes.icm' ftype="tar" />
<param name="max_olap" value="50" />
Expand All @@ -118,6 +118,20 @@
<output name="report_output" file='glimmer_w_icm_trans-table-11_genomic.out' ftype="txt" />
<output name="detailed_output" file='glimmer_w_icm_trans-table-11_genomic.dout' ftype="txt" lines_diff="6" />
</test>
<test expect_num_outputs="1">
<param name="seq_input" value='streptomyces_Tue6071_plasmid_genomic.fasta' />
<param name="icm_input" value='streptomyces_Tu6071_plasmid_genes.icm' ftype="tar" />
<param name="max_olap" value="50" />
<param name="gene_len" value="90" />
<param name="threshold" value="30" />
<param name="gc_percent" value="0.0" />
<param name="linear" value="--linear" />
<param name="no_indep" value="" />
<param name="extend" value="" />
<param name="start_codons" value="atg,gtg,ttg" />
<param name="genbank_gencode" value="11" />
<output name="genes_output" file='glimmer_w_icm_trans-table-11_genomic.fasta' ftype="fasta" />
</test>
</tests>
<help><![CDATA[
**What it does**
Expand Down
24 changes: 17 additions & 7 deletions tools/glimmer/glimmer_wo_icm.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<tool id="glimmer_not_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@">
<tool id="glimmer_not_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
<description>Predict ORFs in prokaryotic genomes (not knowlegde-based)</description>
<expand macro="bio_tools"/>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="bio_tools"/>
<expand macro="requirements"/>
<command><![CDATA[
python '$__tool_directory__/glimmer_wo_icm.py'
Expand Down Expand Up @@ -31,20 +31,20 @@
<param name="threshold" type="integer" value="30" label="Set threshold score for calling as gene. If the in-frame score >= N, then the region is given a number and considered a potential gene." />
<param name="linear" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Assume linear rather than circular genome, i.e., no wraparound" />

<param name="detailed_report" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a detailed gene prediction report as separate file" />
<param name="report" type="boolean" truevalue="" falsevalue="" checked="false" label="Report the classic glimmer table output" />
<param name="detailed_report" type="boolean" checked="false" label="Output a detailed gene prediction report as separate file" />
<param name="report" type="boolean" checked="false" label="Report the classic glimmer table output" />
</inputs>
<outputs>
<data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" />
<data name="prediction" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)">
<filter>report == True</filter>
<filter>report</filter>
</data>
<data name="detailed" format="txt" label="Glimmer3 on ${on_string} (detailed report)">
<filter>detailed_report == True</filter>
<filter>detailed_report</filter>
</data>
</outputs>
<tests>
<test>
<test expect_num_outputs="1">
<param name="input" value="streptomyces_Tue6071_plasmid_genomic.fasta" />
<param name="overlap" value="0" />
<param name="gene_length" value="110" />
Expand All @@ -54,6 +54,16 @@
<param name="report" value="" />
<output name="genes_output" file="glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta" ftype="fasta" />
</test>
<test expect_num_outputs="3">
<param name="input" value="streptomyces_Tue6071_plasmid_genomic.fasta" />
<param name="overlap" value="0" />
<param name="gene_length" value="110" />
<param name="threshold" value="30" />
<param name="linear" value="true" />
<param name="detailed_report" value="true" />
<param name="report" value="true" />
<output name="genes_output" file="glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta" ftype="fasta" />
</test>
</tests>
<help>
<![CDATA[
Expand Down
7 changes: 5 additions & 2 deletions tools/glimmer/macros.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,12 @@
<?xml version="1.0"?>
<macros>
<token name="@TOOL_VERSION@">3.02</token>
<token name="@VERSION_SUFFIX@">2</token>
<token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy@VERSION_SUFFIX@</token>
<token name="@PROFILE_VERSION@">23.1</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="3.02">glimmer</requirement>
<requirement type="package" version="@TOOL_VERSION@">glimmer</requirement>
<requirement type="package" version="1.70">biopython</requirement>
<yield/>
</requirements>
Expand All @@ -12,7 +16,6 @@
<xref type="bio.tools">gemini</xref>
</xrefs>
</xml>
<token name="@WRAPPER_VERSION@">3.02</token>

<xml name="citation">
<citations>
Expand Down
Loading