Mercurial > repos > jjohnson > cistrome_beta

changeset 4:52ed4957ace9 draft

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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
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" />