Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix
changeset 7:7c5b8da3a052 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058
| author | iuc |
|---|---|
| date | Tue, 02 Jan 2018 09:46:28 -0500 |
| parents | 747a789ce63c |
| children | 5fd877e2296b |
| files | hicBuildMatrix.xml macros.xml test-data/raw_qc_report |
| diffstat | 3 files changed, 34 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- a/hicBuildMatrix.xml Sat Dec 30 08:21:48 2017 -0500 +++ b/hicBuildMatrix.xml Tue Jan 02 09:46:28 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> +<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1"> <description>creates a contact matrix</description> <macros> <token name="@BINARY@">hicBuildMatrix</token> @@ -61,6 +61,7 @@ mv ./QCfolder/* $qc.files_path/ && mv $qc.files_path/hicQC.html $qc + && mv $qc.files_path/*.log raw_qc && samtools sort ./unsorted.bam -o sorted.bam ]]> @@ -128,6 +129,7 @@ <filter>outputFormat == 'cool'</filter> </data> <data name="qc" format="html" label="${tool.name} QC"/> + <data name="raw_qc" from_work_dir='raw_qc' label="${tool.name} raw QC" /> </outputs> <tests> <test> @@ -145,6 +147,7 @@ <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/> <output name="outFileName_h5" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/> + <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/> </test> </tests> <help><![CDATA[
--- a/macros.xml Sat Dec 30 08:21:48 2017 -0500 +++ b/macros.xml Tue Jan 02 09:46:28 2018 -0500 @@ -11,7 +11,7 @@ <xml name="citations"> <citations> - <citation type="doi">10.5281/zenodo.1123667</citation> + <citation type="doi">10.5281/zenodo.1133705</citation> <yield /> </citations> </xml>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw_qc_report Tue Jan 02 09:46:28 2018 -0500 @@ -0,0 +1,29 @@ + +File text_matrix.h5 +Pairs considered 983 +Min rest. site distance 300 +Max library insert size 1000 + +# count (percentage w.r.t. total sequenced reads) +Pairs mappable, unique and high quality 300 (30.52) +Pairs used 215 (21.87) +One mate unmapped 506 (51.48) +One mate not unique 13 (1.32) +One mate low quality 164 (16.68) + +# count (percentage w.r.t. mappable, unique and high quality pairs) +dangling end 0 (0.00) +self ligation (removed) 0 (0.00) +One mate not close to rest site 0 (0.00) +same fragment 85 (28.33) +self circle 0 (0.00) +duplicated pairs 0 (0.00) + +# count (percentage w.r.t. total valid pairs used) +inter chromosomal 24 (11.16) +short range < 20kb 61 (28.37) +long range 130 (60.47) +inward pairs 42 (19.53) +outward pairs 66 (30.70) +left pairs 48 (22.33) +right pairs 35 (16.28)