# HG changeset patch
# User jpayne
# Date 1557328214 14400
# Node ID fc7a28de6aa01135d25524c677b753caa7f0c604
# Parent  1667e4c0834450e05c136527be413ce56c9439b9
planemo upload commit 2107f35724b3f897c9414be40a9d14663cba9f4d-dirty

diff -r 1667e4c08344 -r fc7a28de6aa0 2_call_sites.xml
--- 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 "
diff -r 1667e4c08344 -r fc7a28de6aa0 3_filter_regions.xml
--- 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   &&
diff -r 1667e4c08344 -r fc7a28de6aa0 4_merge_sites.xml
--- 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
diff -r 1667e4c08344 -r fc7a28de6aa0 5_call_consensus.xml
--- 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)"
diff -r 1667e4c08344 -r fc7a28de6aa0 6_merge_vcfs.xml
--- 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"
diff -r 1667e4c08344 -r fc7a28de6aa0 7_smp_matrix.xml
--- 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