opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge pull request #9389 from mvdbeek/fix_tar_to_directory_dependency

Browse Source 
[20.01] Fix dependency for CONVERTER_tar_to_directory
This commit is contained in:
Marius van den Beek
2020-02-19 20:26:22 +01:00
committed by GitHub
parent 8665316cac 747eabdd2e
commit b43c090d35
7 changed files with 9 additions and 10 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
+1 -1
View File
@@ -1,6 +1,6 @@
<tool id="CONVERTER_fastq_to_fqtoc0" name="Convert FASTQ files to seek locations" version="1.0.1" hidden="true" profile="16.04">
<requirements>
<requirement type="package" version="19.09">galaxy-util</requirement>
<requirement type="package" version="19.9">galaxy-util</requirement>
</requirements>
<command>python '$__tool_directory__/fastq_to_fqtoc.py' '$input1' '$output1'</command>
<inputs>
lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
+3 -3
View File
@@ -1,7 +1,7 @@
<tool id="tabular_to_dbnsfp" name="Convert tabular to dbnsfp" version="1.0.1" profile="16.04">
<description></description>
<requirements>
<requirement type="package" version="3.7">python</requirement>
<requirement type="package" version="0.15.4">pysam</requirement>
</requirements>
<command>python '$__tool_directory__/tabular_to_dbnsfp.py' '$input' '$dbnsfp.extra_files_path/dbNSFP.gz'</command>
<inputs>
@@ -12,8 +12,8 @@
</outputs>
<tests>
<test>
<param name="input" format="tabular" value="gtf_filter_by_attribute_values_list_in3.tabular"/>
<output name="dbnsfp" format="snpsiftdbnsfp" value="gtf_filter_by_attribute_values_list_in3.snpsiftdbnsfp"/>
<param name="input" format="tabular" value="vcf2pgSnp_input.vcf"/>
<output name="dbnsfp" format="snpsiftdbnsfp" value="vcf2pgSnp_input.vcf.snpsiftdbnsfp"/>
</test>
</tests>
<help>
lib/galaxy/datatypes/converters/tar_to_directory.xml
+1 -1
View File
@@ -1,7 +1,7 @@
<tool id="CONVERTER_tar_to_directory" name="Convert tar to directory" version="1.0.1" profile="17.05">
<!-- Don't use tar directly so we can verify safety of results - tar -xzf '$input1'; -->
<requirements>
<requirement type="package" version="19.09">galay-util</requirement>
<requirement type="package" version="19.9">galaxy-util</requirement>
</requirements>
<command>
mkdir '$output1.files_path';
lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
+1 -1
View File
@@ -2,7 +2,7 @@
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<!-- Used on the metadata edit page. -->
<requirements>
<requirement type="package" version="19.09">galaxy-util</requirement>
<requirement type="package" version="19.9">galaxy-util</requirement>
<requirement type="package" version="0.8.6">bx-python</requirement>
</requirements>
<command>python '$__tool_directory__/wiggle_to_simple_converter.py' '$input' '$out_file1'</command>
lib/galaxy/tools/__init__.py
+1 -2
View File
@@ -159,8 +159,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
"substitutions1",
"find_diag_hits",
"cufflinks",
# Tools improperly migrated to the tool shed (iuc)
"tabular_to_dbnsfp",
# Tools improperly migrated using Galaxy (from shed other)
"column_join",
"gd_coverage_distributions", # Genome Diversity tools from miller-lab
@@ -189,6 +187,7 @@ GALAXY_LIB_TOOLS_VERSIONED = {
"aggregate_scores_in_intervals2": packaging.version.parse("1.1.4"),
"CONVERTER_fastq_to_fqtoc0": packaging.version.parse("1.0.1"),
"CONVERTER_tar_to_directory": packaging.version.parse("1.0.1"),
"tabular_to_dbnsfp": packaging.version.parse("1.0.1"),
}
tools/filters/wiggle_to_simple.xml
+1 -1
View File
@@ -1,7 +1,7 @@
<tool id="wiggle2simple1" name="Wiggle-to-Interval" version="1.0.1" profile="16.04">
<description>converter</description>
<requirements>
<requirement type="package" version="19.09">galaxy-util</requirement>
<requirement type="package" version="19.9">galaxy-util</requirement>
<requirement type="package" version="0.8.6">bx-python</requirement>
</requirements>
<command>python '$__tool_directory__/wiggle_to_simple.py' '$input' '$out_file1'</command>
tools/stats/aggregate_binned_scores_in_intervals.xml
+1 -1
View File
@@ -1,7 +1,7 @@
<tool id="aggregate_scores_in_intervals2" name="Aggregate datapoints" version="1.1.4" profile="16.04">
<description>Appends the average, min, max of datapoints per interval</description>
<requirements>
<requirement type="package" version="19.09">galaxy-util</requirement>
<requirement type="package" version="19.9">galaxy-util</requirement>
<requirement type="package" version="0.8.6">bx-python</requirement>
</requirements>
<command>