diff samtools/samtools_sort/macros.xml @ 28:060c2129612f draft

Uploaded

--- a/samtools/samtools_sort/macros.xml	Thu Oct 03 11:19:14 2019 -0400
+++ b/samtools/samtools_sort/macros.xml	Thu Oct 03 11:27:47 2019 -0400
@@ -1,137 +1,16 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
+            <requirement type="package" version="1.2">samtools</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">1.9</token>
-    <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
-    <token name="@PREPARE_IDX@"><![CDATA[
-        ##prepare input and indices 
-        ln -s '$input' infile &&
-        #if $input.is_of_type('bam'):
-            #if str( $input.metadata.bam_index ) != "None":
-                ln -s '${input.metadata.bam_index}' infile.bai &&
-            #else:
-                samtools index infile infile.bai &&
-            #end if
-        #elif $input.is_of_type('cram'):
-            #if str( $input.metadata.cram_index ) != "None":
-                ln -s '${input.metadata.cram_index}' infile.crai &&
-            #else:
-                samtools index infile infile.crai &&
-            #end if
-        #end if
-    ]]></token>
-    <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
-        ##prepare input and indices 
-        #for $i, $bam in enumerate( $input_bams ):
-            ln -s '$bam' '${i}' &&
-            #if $bam.is_of_type('bam'):
-                #if str( $bam.metadata.bam_index ) != "None":
-                    ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
-                #else:
-                    samtools index '${i}' '${i}.bai' &&
-                #end if
-            #elif $bam.is_of_type('cram'):
-                #if str( $bam.metadata.cram_index ) != "None":
-                    ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
-                #else:
-                    samtools index '${i}' '${i}.crai' &&
-                #end if
-            #end if
-        #end for
-    ]]></token>
-    <token name="@PREPARE_FASTA_IDX@"><![CDATA[
-        ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")
-        ##and sets the -t/-T parameters accordingly:
-        ##- in case of history a symbolic link is used because samtools (view) will generate
-        ##  the index which might not be possible in the directory containing the fasta file
-        ##- in case of cached the absolute path is used which allows to read the cram file
-        ##  without specifying the reference
-        #if $addref_cond.addref_select == "history":
-            ln -s '${addref_cond.ref}' reference.fa &&
-            samtools faidx reference.fa &&
-            #set reffa="reference.fa"
-            #set reffai="reference.fa.fai"
-        #elif $addref_cond.addref_select == "cached":
-            #set reffa=str($addref_cond.ref.fields.path)
-            #set reffai=str($addref_cond.ref.fields.path)+".fai"
-        #else
-            #set reffa=None
-            #set reffai=None
-        #end if
-    ]]></token>
-    <token name="@ADDTHREADS@"><![CDATA[
-        ##compute the number of ADDITIONAL threads to be used by samtools (-@)
-        addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
-    ]]></token>
-    <token name="@ADDMEMORY@"><![CDATA[
-        ##compute the number of memory available to samtools sort (-m)
-        ##use only 75% of available: https://github.com/samtools/samtools/issues/831
-        addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && 
-        ((addmemory=addmemory*75/100)) &&
-    ]]></token>
-    <xml name="seed_input">
-       <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> 
-    </xml>
-    <xml name="flag_options">
-        <option value="1">read is paired</option>
-        <option value="2">read is mapped in a proper pair</option>
-        <option value="4">read is unmapped</option>
-        <option value="8">mate is unmapped</option>
-        <option value="16">read reverse strand</option>
-        <option value="32">mate reverse strand</option>
-        <option value="64">read is the first in a pair</option>
-        <option value="128">read is the second in a pair</option>
-        <option value="256">alignment or read is not primary</option>
-        <option value="512">read fails platform/vendor quality checks</option>
-        <option value="1024">read is a PCR or optical duplicate</option>
-        <option value="2048">supplementary alignment</option>
-    </xml>
-
-    <!-- region specification macros and tokens for tools that allow the specification 
-         of region by bed file / space separated list of regions -->
-    <token name="@REGIONS_FILE@"><![CDATA[
-        #if $cond_region.select_region == 'tab':
-            -t '$cond_region.targetregions'
-        #end if
-    ]]></token>
-    <token name="@REGIONS_MANUAL@"><![CDATA[
-        #if $cond_region.select_region == 'text':
-            #for $i, $x in enumerate($cond_region.regions_repeat):
-               '${x.region}'
-            #end for
-        #end if
-    ]]></token>
-    <xml name="regions_macro">
-        <conditional name="cond_region">
-            <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
-                <option value="no" selected="True">No</option>
-                <option value="text">Manualy specify regions</option>
-                <option value="tab">Regions from tabular file</option>
-            </param>
-            <when value="no"/>
-            <when value="text">
-                <repeat name="regions_repeat" min="1" default="1" title="Regions">
-                    <param name="region" type="text" label="region" help="format chr:from-to">
-                        <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
-                    </param>
-                </repeat>
-            </when>
-            <when value="tab">
-                <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" />
-            </when>
-        </conditional>
-    </xml>
-
     <xml name="citations">
         <citations>
             <citation type="bibtex">
                 @misc{SAM_def,
                 title={Definition of SAM/BAM format},
-                url = {https://samtools.github.io/hts-specs/},}
+                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>
@@ -162,11 +41,30 @@
         </citations>
     </xml>
     <xml name="version_command">
-        <version_command><![CDATA[samtools 2>&1 | grep Version]]></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>