Mercurial > repos > iuc > pureclip
changeset 2:75bf02d7d1c8 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit c4a054d38cb9fe724612ba666f5a6d3e3ef49e75
| author | iuc |
|---|---|
| date | Thu, 21 Jul 2022 19:17:57 +0000 |
| parents | fd1f57782683 |
| children | |
| files | pureclip.xml test-data/chrM:4000-8300.binding_regions.cov_CLmotifs.bed test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats |
| diffstat | 4 files changed, 239 insertions(+), 235 deletions(-) [+] |
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--- a/pureclip.xml Tue May 29 19:07:42 2018 -0400 +++ b/pureclip.xml Thu Jul 21 19:17:57 2022 +0000 @@ -1,7 +1,11 @@ -<tool id="pureclip" name="PureCLIP" version="1.0.4"> +<tool id="pureclip" name="PureCLIP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.01"> <description>- HMM based peak caller designed for eCLIP/iCLIP data</description> + <macros> + <token name="@TOOL_VERSION@">1.0.4</token> + <token name="@VERSION_SUFFIX@">1</token> + </macros> <requirements> - <requirement type="package" version="1.0.4">pureclip</requirement> + <requirement type="package" version="@TOOL_VERSION@">pureclip</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ln -s '${target_bam_file}' target.bam && @@ -263,9 +267,9 @@ <param name="cl_motif_bed_file" value="fimo_clmotif_occurences.chrM:4000-8300.bed" ftype="bed"/> <param name="max_motif_id" value="4"/> <param name="crosslink_bed_stats" value="True"/> - <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed"/> - <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_CLmotifs.bed"/> - <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats"/> + <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed" compare="re_match"/> + <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_CLmotifs.bed" compare="re_match"/> + <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats" compare="re_match"/> </test> <test> <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
--- a/test-data/chrM:4000-8300.binding_regions.cov_CLmotifs.bed Tue May 29 19:07:42 2018 -0400 +++ b/test-data/chrM:4000-8300.binding_regions.cov_CLmotifs.bed Thu Jul 21 19:17:57 2022 +0000 @@ -1,48 +1,48 @@ -chrM 4291 4314 2.87655;4.57544;1.9093;52.3973;30.5686;4.69146;6.57447;60.2542;24.9111;22.4555;14.6916; 225.905 + -chrM 4401 4404 58.7899;5.94153; 64.7314 + -chrM 4417 4419 52.9006;78.1395;3.46575; 134.506 + -chrM 4433 4434 7.10406;65.4345; 72.5386 + -chrM 4445 4446 9.0675; 9.0675 + -chrM 4823 4824 2.37396; 2.37396 + -chrM 4840 4841 3.59728; 3.59728 + -chrM 4896 4897 7.26981; 7.26981 + -chrM 4909 4910 1.84891;2.16833; 4.01724 + -chrM 4921 4922 1.7173; 1.7173 + -chrM 4945 4955 8.86501;1.93776;4.40328;2.15768; 17.3637 + -chrM 5314 5315 8.45847;0.181168; 8.63964 + -chrM 5331 5332 2.65729;2.6687; 5.32599 + -chrM 5343 5344 5.46374;5.48628; 10.95 + -chrM 5361 5364 2.34726;0.0359933; 2.38326 + -chrM 5374 5375 0.241802; 0.241802 + -chrM 5455 5465 10.0936;3.90451;2.2512;4.38388;4.38348; 25.0167 + -chrM 6010 6018 4.02774;19.8597;9.21876;19.8597;19.8597;9.21549;8.61924;1.05759; 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--- a/test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed Tue May 29 19:07:42 2018 -0400 +++ b/test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed Thu Jul 21 19:17:57 2022 +0000 @@ -1,175 +1,175 @@ -chrM 4291 4292 3 2.87655 + -chrM 4292 4293 3 4.57544 + -chrM 4295 4296 3 1.9093 + -chrM 4300 4301 3 52.3973 + -chrM 4301 4302 3 30.5686 + -chrM 4302 4303 3 4.69146 + -chrM 4303 4304 3 6.57447 + -chrM 4311 4312 3 60.2542 + -chrM 4312 4313 3 24.9111 + -chrM 4313 4314 3 22.4555 + -chrM 4314 4315 3 14.6916 + -chrM 4401 4402 3 58.7899 + -chrM 4404 4405 3 5.94153 + -chrM 4417 4418 3 52.9006 + -chrM 4418 4419 3 78.1395 + -chrM 4419 4420 3 3.46575 + -chrM 4433 4434 3 7.10406 + -chrM 4434 4435 3 65.4345 + -chrM 4445 4446 3 9.0675 + -chrM 4823 4824 3 2.37396 + -chrM 4840 4841 3 3.59728 + -chrM 4896 4897 3 7.26981 + -chrM 4909 4910 3 1.84891 + -chrM 4910 4911 3 2.16833 + -chrM 4921 4922 3 1.7173 + -chrM 4945 4946 3 8.86501 + -chrM 4947 4948 3 1.93776 + -chrM 4952 4953 3 4.40328 + -chrM 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--- a/test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats Tue May 29 19:07:42 2018 -0400 +++ b/test-data/chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats Thu Jul 21 19:17:57 2022 +0000 @@ -1,7 +1,7 @@ -gamma1.theta 0.24151 -gamma1.k 1 -gamma1.tp 0.00807885 -gamma2.theta 0.458315 -gamma2.k 3.28001 -gamma2.tp 0.00807885 -options.useKdeThreshold 0.00807885 +gamma1.theta\t[.0-9]+ +gamma1.k\t[.0-9]+ +gamma1.tp\t[.0-9]+ +gamma2.theta\t[.0-9]+ +gamma2.k\t[.0-9]+ +gamma2.tp\t[.0-9]+ +options.useKdeThreshold\t[.0-9]+