diff cloudmap.xml @ 8:d79fe626c6fd

upgrade to v0.1.7.1

--- a/cloudmap.xml	Tue Sep 22 22:36:41 2015 +0200
+++ b/cloudmap.xml	Thu Oct 22 15:34:23 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="nacreousmap" name="NacreousMap" version="0.1.7.0">
+<tool id="nacreousmap" name="NacreousMap" version="0.1.7.1">
   <description>Map causative mutations by multi-variant linkage analysis.</description>
   <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
@@ -105,7 +105,7 @@
             <option value="">preserve relative contig sizes</option>
             <option value="--fit-width">scale each contig to fit the plot width</option>
           </param>
-          <param name="span" type="text" label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1)" help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." />
+          <param name="span" type="text" label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1, specify 0 to prevent calculation)" help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." />
           <expand macro="scatter_colors" />
         </when>
         <when value="-p">
@@ -156,7 +156,7 @@
         <option value="">preserve relative contig sizes</option>
         <option value="--fit-width">scale each contig to fit the plot width</option>
       </param>
-      <param name="span" type="text" label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1)" help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." />
+      <param name="span" type="text" label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1, specify 0 to prevent calculation)" help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." />
       <expand macro="hist_colors" />
       <expand macro="scatter_colors" />
     </macro>
@@ -213,7 +213,7 @@
             <param name="sample" type="text" label="mapping sample name" help="the sample to perform mutation mapping for" />
             <param name="related_parent_sample" type="text" label="name of the related parent sample" help="the sample that provides variants present in your original mutant strain or in an ancestor (like the pre-mutagenesis strain); leave blank if not available" />
             <param name="unrelated_parent_sample" type="text" label="name of the unrelated parent sample" help="the sample that provides variants present in the unrelated mapping strain (or in an ancestor of it) used in the mapping cross; leave blank if not available" />
-            <param name="infer_missing" type="boolean" checked="false" truevalue="--infer-missing" falsevalue="" label="Infer alleles for missing parent" help="if variant data for either the related or the unrelated parent strain is not available, the tool can try to infer the alleles present in that parent from the allele spectrum found in the mapping sample. This is an EXPERIMENTAL option that will give a benefit only in certain situations. Enable at your own risk." />
+            <param name="infer_missing" type="boolean" checked="false" truevalue="--infer-missing" falsevalue="" label="Infer alleles for missing parent" help="if variant data for either the related or the unrelated parent strain is not available, the tool can try to infer the alleles present in that parent from the allele spectrum found in the mapping sample. Use with caution on carefully filtered variant lists only!" />
             <expand macro="vaf_unconditional" />
             <param name="tabfile" type="select" label="additional per-variant output file" help="You can either choose to produce a tabular per-variant report, which is useful for fast replotting with different plot settings or a vcf-like CloudMap-compatibility file that can be used as input for the CloudMap Hawaiian Variant Mapping tool as an alternative plotting tool.">
               <option value="">Do not generate per-variant output</option>