spades: add OMP_THREAD_LIMIT (#4711)

* spades: add OMP_THREAD_LIMIT

despite the `-t` argument spades may run only sequential.
you find in the logs:

```
Maximum # of threads to use (adjusted due to OMP capabilities): 1
```

* spades: remove URL that times out from docs

tools/spades/biosyntheticspades.xml

@@ -16,6 +16,7 @@
 #end if
 @PREPROCESS_NANOPORE_PACBIO_FILES@
 
+@OMP_THREADS@
 ## run
 spades.py --bio
     -o 'output'
@@ -175,7 +176,7 @@ A detailed description can be found in the `output section <https://github.com/a
 
 **References**
 
-More information can be found on `github <https://github.com/ablab/spades>`_  and on the `project website <http://cab.spbu.ru/software/biosyntheticspades>`_.
+More information can be found on `github <https://github.com/ablab/spades>`_.
     ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1101/gr.243477.118</citation>

tools/spades/coronaspades.xml

@@ -19,6 +19,7 @@
 @PREPROCESS_SANGER_FILES@
 
 
+@OMP_THREADS@
 ## run
 coronaspades.py
     -o 'output'
@@ -162,7 +163,7 @@ Input data can be provided as interlaced, forward and reverse, merged and unpair
 
 **References**
 
-More information can be found on `github <https://github.com/ablab/spades>`_  and on the `project website <https://cab.spbu.ru/software/coronaspades/>`_.
+More information can be found on `github <https://github.com/ablab/spades>`_.
     ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1093/bioinformatics/btab597</citation>

tools/spades/macros.xml

@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.15.4</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
@@ -43,6 +43,9 @@
         </param>
     </xml>
 
+<token name="@OMP_THREADS@"><![CDATA[
+export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
+]]></token>
 
 <!-- PREPARE INPUT FILES-->
 
@@ -738,7 +741,7 @@ A detailed description can be found in the `input section <https://github.com/ab
 SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
     </token>
     <token name="@IONTORRENT@"><![CDATA[
-The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our `recommendation for long reads <https://cab.spbu.ru/files/release3.12.0/manual.html#sec3.4>`_ (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o <previous_output_dir>. Do not forget to copy contigs and scaffolds from the previous run. We're planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions.
+The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our `recommendation for long reads <https://github.com/ablab/spades#sec3.4>`_ (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o <previous_output_dir>. Do not forget to copy contigs and scaffolds from the previous run. We're planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions.
 
 You may need no error correction for Hi-Q enzyme at all. However, we suggest trying to assemble your data with and without error correction and select the best variant.
 

tools/spades/metaplasmidspades.xml

@@ -19,6 +19,7 @@
 @PREPROCESS_CONTIGS_FILES@
 @PREPROCESS_ASSEMBLY_GRAPH_FILES@
 
+@OMP_THREADS@
 ## run
 spades.py --meta --plasmid
     -o 'output'
@@ -233,7 +234,7 @@ metaplasmidSPAdes is a subtool for assembling plasmids from metagenomic data set
 
 **References**
 
-More information can be found on `github <https://github.com/ablab/spades>`_  and on the `project website <http://cab.spbu.ru/software/spades>`_.
+More information can be found on `github <https://github.com/ablab/spades>`_.
     ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1101/gr.241299.118</citation>

tools/spades/metaspades.xml

@@ -16,6 +16,7 @@
 #end if
 @PREPROCESS_NANOPORE_PACBIO_FILES@
 
+@OMP_THREADS@
 ## run
 metaspades.py
     -o 'output'
@@ -185,7 +186,7 @@ metaSPAdes is a subtool for assembling metagenomic data sets.
 
 **References**
 
-More information can be found on `github <https://github.com/ablab/spades>`_ and on the `project website <http://cab.spbu.ru/software/meta-spades>`_.
+More information can be found on `github <https://github.com/ablab/spades>`_.
     ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1101/gr.213959.116</citation>

tools/spades/metaviralspades.xml

@@ -19,6 +19,7 @@
 @PREPROCESS_CONTIGS_FILES@
 @PREPROCESS_ASSEMBLY_GRAPH_FILES@
 
+@OMP_THREADS@
 ## run
 spades.py --metaviral
     -o 'output'
@@ -233,7 +234,7 @@ metaplasmidSPAdes is a subtool for assembling plasmids from metagenomic data set
 
 **References**
 
-More information can be found on `github <https://github.com/ablab/spades>`_  and on the `project website <http://cab.spbu.ru/software/spades>`_.
+More information can be found on `github <https://github.com/ablab/spades>`_.
     ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1101/gr.241299.118</citation>

tools/spades/plasmidspades.xml

@@ -19,6 +19,7 @@
 @PREPROCESS_CONTIGS_FILES@
 @PREPROCESS_ASSEMBLY_GRAPH_FILES@
 
+@OMP_THREADS@
 ## run
 plasmidspades.py
     $operation_mode
@@ -377,7 +378,7 @@ plasmidSPAdes is a subtool for assembling plasmid data sets.
 
 **References**
 
-More information can be found on `github <https://github.com/ablab/spades>`_  and on the `project website <http://cab.spbu.ru/software/plasmid-spades>`_.
+More information can be found on `github <https://github.com/ablab/spades>`_.
     ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1093/bioinformatics/btw493</citation>

tools/spades/rnaspades.xml

@@ -18,7 +18,7 @@
 @PREPROCESS_CONTIGS_FILES@
 @PREPROCESS_FL_RNA_FILES@
 
-
+@OMP_THREADS@
 ## run
 rnaspades.py
     -o 'output'    
@@ -238,7 +238,7 @@ and strand-specificity. Transcript quantification for each sample can be done af
 
 **References**
 
-More information can be found on on `github <https://github.com/ablab/spades>`_ and on the `project website <http://cab.spbu.ru/software/rnaspades>`_.
+More information can be found on on `github <https://github.com/ablab/spades>`_.
     ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1101/420208</citation>

tools/spades/rnaviralspades.xml

@@ -18,6 +18,7 @@
 @PREPROCESS_CONTIGS_FILES@
 @PREPROCESS_SANGER_FILES@
 
+@OMP_THREADS@
 ## run
 spades.py --rnaviral
     -o 'output'    
@@ -351,7 +352,7 @@ rnaviralSPAdes is a pipeline specially designed for de novo assembler tailored f
 
 **References**
 
-More information are available on `github <https://github.com/ablab/spades>`_ and on the `project website <http://cab.spbu.ru/software/spades>`_.
+More information are available on `github <https://github.com/ablab/spades>`_.
     ]]></help>
     <expand macro="citations"/>
 </tool>

tools/spades/spades.xml

@@ -18,6 +18,7 @@
 @PREPROCESS_CONTIGS_FILES@
 @PREPROCESS_SANGER_FILES@
 
+@OMP_THREADS@
 ## run
 spades.py
     $operation_mode
@@ -731,7 +732,7 @@ spades.py
 
 **References**
 
-More information are available on `github <https://github.com/ablab/spades>`_ and on the `project website <http://cab.spbu.ru/software/spades>`_.
+More information are available on `github <https://github.com/ablab/spades>`_.
     ]]></help>
     <expand macro="citations">
             <citation type="doi">10.1089/cmb.2012.0021</citation>