Mercurial > repos > jjohnson > cistrome_beta
changeset 4:52ed4957ace9 draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/cistrome_beta commit c7ec1c7f1eb5f67fcd76e365b3cd0b35ef3509e6-dirty
author | jjohnson |
---|---|
date | Thu, 22 Mar 2018 10:48:43 -0400 (2018-03-22) |
parents | 067573bac905 |
children | c119110a5b47 |
files | beta_basic.xml beta_macros.xml beta_minus.xml beta_plus.xml |
diffstat | 4 files changed, 13 insertions(+), 10 deletions(-) [+] |
line wrap: on
line diff
--- a/beta_basic.xml Thu Mar 22 08:48:00 2018 -0400 +++ b/beta_basic.xml Thu Mar 22 10:48:43 2018 -0400 @@ -10,7 +10,7 @@ #include source=$common_opts# #include source=$genome_opts# #include source=$extended_opts# - &> $log + #include source=$write_log# ]]></command> <inputs> <expand macro="common_params" /> @@ -45,12 +45,12 @@ </output> <output name="uptargetsoutput"> <assert_contents> - <has_text_matching expression="chr19\t4675243\t4723855\tNM_139159\t1.1.*\t-\tDPP" /> + <has_text_matching expression="chr19\t47990890\t48018515\tNR_038457\t4.*\t-\tNAPA" /> </assert_contents> </output> <output name="uptargetpeaks"> <assert_contents> - <has_text_matching expression="chr19\t4723422\t4724314\tregion_9\tNM_139159\tDPP9\t13\t0.6.*" /> + <has_text_matching expression="chr19\t47950633\t47951639\tNR_038457\tNAPA\t-67379\t0.04\d+" /> </assert_contents> </output> </test>
--- a/beta_macros.xml Thu Mar 22 08:48:00 2018 -0400 +++ b/beta_macros.xml Thu Mar 22 10:48:43 2018 -0400 @@ -163,6 +163,9 @@ --gname2" #end if </template> + <template name="write_log"> + | tee $log | grep 'total time' > /dev/null + </template> <token name="@EXTERNAL_DOCUMENTATION@">
--- a/beta_minus.xml Thu Mar 22 08:48:00 2018 -0400 +++ b/beta_minus.xml Thu Mar 22 10:48:43 2018 -0400 @@ -9,7 +9,7 @@ BETA minus #include source=$common_opts# #include source=$genome_opts# - &> $log + #include source=$write_log# ]]></command> <inputs> <expand macro="common_params" />
--- a/beta_plus.xml Thu Mar 22 08:48:00 2018 -0400 +++ b/beta_plus.xml Thu Mar 22 10:48:43 2018 -0400 @@ -12,12 +12,12 @@ #include source=$ref_genome_seq_opts# #include source=$extended_opts# --mn $motifs - &> $log && - mkdir -p $motifresult.extra_files_path && - cp BETA_OUTPUT/motifresult/betamotif.html $motifresult && - cp BETA_OUTPUT/motifresult/*.js $motifresult.extra_files_path && - cp BETA_OUTPUT/motifresult/*.css $motifresult.extra_files_path && - cp -r BETA_OUTPUT/motifresult/img $motifresult.extra_files_path + #include source=$write_log# + && mkdir -p $motifresult.extra_files_path + && cp BETA_OUTPUT/motifresult/betamotif.html $motifresult + && cp BETA_OUTPUT/motifresult/*.js $motifresult.extra_files_path + && cp BETA_OUTPUT/motifresult/*.css $motifresult.extra_files_path + && cp -r BETA_OUTPUT/motifresult/img $motifresult.extra_files_path ]]></command> <inputs> <expand macro="common_params" />