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

Fixed the unexpected behaviour due to --assembly parameter of pairtools parse #5953

Merged
merged 6 commits into from
Apr 16, 2024
Merged

Fixed the unexpected behaviour due to --assembly parameter of pairtools parse #5953

Changes from 3 commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
4d249f4
Fixed Label Swapping issue
SaimMomin12 Apr 9, 2024
988391f
Debugging of --assembly name parameter
SaimMomin12 Apr 16, 2024
7baf28d
Merge branch 'galaxyproject:main' into pairtools_parse1
SaimMomin12 Apr 16, 2024
ef7ae57
Eliminated conditional for assembly
SaimMomin12 Apr 16, 2024
8a37097
Added a test for assembly name
SaimMomin12 Apr 16, 2024
d1296d7
Version bump for parse
SaimMomin12 Apr 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
15 changes: 13 additions & 2 deletions tools/pairtools/parse.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,9 @@
pairtools parse
'$sam_path'
-c '$chroms_path'
$assembly
#if str( $assembly_selection.assembly_name_selector ) == "yes":
--assembly $assembly_name
SaimMomin12 marked this conversation as resolved.
Show resolved Hide resolved
#end if
-o '$output_parsed_pairs'
--min-mapq '$min_mapq'
--max-molecule-size '$max_molecule_size'
Expand All @@ -27,7 +29,16 @@
<inputs>
<param name="sam_path" type="data" format="sam,bam" label="Input SAM/BAM file" help="Input SAM or BAM file with paired-end sequence alignments of Hi-C molecules."/>
<param name="chroms_path" argument="-c" type="data" format="tabular" label="Input a chromosome order file" help="Chromosome order used to flip interchromosomal mates. Any scaffolds not listed will be ordered lexicographically."/>
<param name="assembly" type="text" value="" label="Input a name of a genome assembly" help="Name of genome assembly (e.g. hg19, mm10) to store in the pairs header"></param>
<conditional name="assembly_selection">
SaimMomin12 marked this conversation as resolved.
Show resolved Hide resolved
<param name="assembly_name_selector" label="Enter a assembly name" help="Input a custom assembly name" type="select">
<option value="yes">Yes</option>
<option value="no" selected="true">No</option>
</param>
<when value="yes">
<param name="assembly_name" type="text" value="" label="Input a name of genome assembly" optional="false" help="Name of genome assembly (e.g. hg19, mm10) to store in the pairs header"></param>
</when>
<when value="no"></when>
</conditional>
<param argument="--min-mapq" type="integer" value="40" min="0" label="Minimal MAPQ" help="Minimal MAPQ score to consider a read as uniquely mapped."/>
<param argument="--max-molecule-size" type="integer" min="0" value="750" label="Input the maximal size of a Hi-C molecule" help="The maximal size of a Hi-C molecule; used to rescue single ligations(from molecules with three alignments) and to rescue complex ligations."></param>
<param argument="--drop-readid" type="boolean" truevalue="--drop-readid" falsevalue="" checked="False" label="Do not add read ids to the output"></param>
Expand Down