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changeset 48:fc7a28de6aa0

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planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty
author jpayne
date Wed, 08 May 2019 11:10:14 -0400
parents 1667e4c08344
children ebfa7fd256aa
files 2_call_sites.xml 3_filter_regions.xml 4_merge_sites.xml 5_call_consensus.xml 6_merge_vcfs.xml 7_smp_matrix.xml
diffstat 6 files changed, 0 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/2_call_sites.xml	Tue May 07 16:12:09 2019 -0400
+++ b/2_call_sites.xml	Wed May 08 11:10:14 2019 -0400
@@ -11,7 +11,6 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
     export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
-    # env &&
     python $__tool_directory__/snp-cache.py snp_sitecalls 
         "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)"
         -c "
--- a/3_filter_regions.xml	Tue May 07 16:12:09 2019 -0400
+++ b/3_filter_regions.xml	Wed May 08 11:10:14 2019 -0400
@@ -9,7 +9,6 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
-        # env &&
         mkdir -p ./samples/sample/                      &&
         cp $calls ./samples/sample/var.flt.vcf      &&
         echo "\$PWD/samples/sample" > ./alignment.txt   &&
--- a/4_merge_sites.xml	Tue May 07 16:12:09 2019 -0400
+++ b/4_merge_sites.xml	Wed May 08 11:10:14 2019 -0400
@@ -9,7 +9,6 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
-        # env &&
         python $__tool_directory__/snp-wind.py ./
                 #for $call in $calls
                     -n $call.element_identifier -f $call
--- a/5_call_consensus.xml	Tue May 07 16:12:09 2019 -0400
+++ b/5_call_consensus.xml	Wed May 08 11:10:14 2019 -0400
@@ -8,7 +8,6 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
-        # env &&
         #set $identifier = $call_pileup.name.split(' ')[0]
         python $__tool_directory__/snp-cache.py snp_consenus_calls
             "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
--- a/6_merge_vcfs.xml	Tue May 07 16:12:09 2019 -0400
+++ b/6_merge_vcfs.xml	Wed May 08 11:10:14 2019 -0400
@@ -10,7 +10,6 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
-        # env &&
         ls -lah \$CONDA_DEFAULT_ENV/bin &&
         ls -lah \$CONDA_DEFAULT_ENV/lib &&
         python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
--- a/7_smp_matrix.xml	Tue May 07 16:12:09 2019 -0400
+++ b/7_smp_matrix.xml	Wed May 08 11:10:14 2019 -0400
@@ -9,7 +9,6 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
-        # env &&
         python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"
             #for $fa in sorted($cons, key=lambda f: f.element_identifier)
                 -n $fa.element_identifier -f $fa