# HG changeset patch
# User jbrayet
# Date 1447847858 18000
# Node ID 6024acc63f80ec20598e6a8a1a47a2ab846dcb6c
# Parent  6829a4f31c3f5ac824dac924253c1a43acc946f2
Deleted selected files

diff -r 6829a4f31c3f -r 6024acc63f80 macros.xml
--- a/macros.xml	Wed Nov 18 05:55:12 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-<macros>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="0.1">docker_samtools</requirement>
-            <container type="docker">samtools:1.0</container>
-            <yield/>
-        </requirements>
-    </xml>
-    <xml name="citations">
-        <citations>
-            <citation type="bibtex">
-                @misc{SAM_def,
-                title={Definition of SAM/BAM format},
-                url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
-            </citation>
-            <citation type="doi">10.1093/bioinformatics/btp352</citation>
-            <citation type="doi">10.1093/bioinformatics/btr076</citation>
-            <citation type="doi">10.1093/bioinformatics/btr509</citation>
-            <citation type="bibtex">
-                @misc{Danecek_et_al,
-                Author={Danecek, P., Schiffels, S., Durbin, R.},
-                title={Multiallelic calling model in bcftools (-m)},
-                url = {http://samtools.github.io/bcftools/call-m.pdf},}
-            </citation>
-            <citation type="bibtex">
-                @misc{Durbin_VCQC,
-                Author={Durbin, R.},
-                title={Segregation based metric for variant call QC},
-                url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
-            </citation>
-            <citation type="bibtex">
-                @misc{Li_SamMath,
-                Author={Li, H.},
-                title={Mathematical Notes on SAMtools Algorithms},
-                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
-            </citation>
-            <citation type="bibtex">
-                @misc{SamTools_github,
-                title={SAMTools GitHub page},
-                url = {https://github.com/samtools/samtools},}
-            </citation>
-        </citations>
-    </xml>
-    <xml name="version_command">
-        <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
-    </xml>
-    <xml name="stdio">
-        <stdio>
-            <exit_code range="1:" level="fatal" description="Error" />
-        </stdio>
-    </xml>
-    <token name="@no-chrom-options@">
------
-
-.. class:: warningmark
-
-**No options available? How to re-detect metadata**
-
-If you see a &quot;No options available&quot; within the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
-
-1. Click on the **pencil** icon adjacent to the dataset in the history
-2. A new menu will appear in the center pane of the interface
-3. Click **Datatype** tab
-4. Set **New Type** to **BAM**
-5. Click **Save**
-
-The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
-
-    </token>
-
-</macros>